Engineered human-endogenous virus-like particles and methods of use thereof for delivery to cells

ABSTRACT

Human-derived virus-like particles (heVLPs), comprising a membrane comprising a phospholipid bilayer with one or more HERV-derived envelope proteins on the external side; one or more HERV-derived GAG proteins in the heVLP core, and a cargo molecule, e.g., a biomolecule and/or chemical cargo molecule, disposed in the core of the heVLP on the inside of the membrane, wherein the heVLP does not comprise a gag protein, except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome, and methods of use thereof for delivery of the cargo molecule to cells.

CLAIM OF PRIORITY

This application is a continuation of U.S. patent application Ser. No. 17/617,490, filed Dec. 8, 2021, which is a § 371 National Stage Application of PCT/US2020/037740, filed Jun. 15, 2020, which claims the benefit of U.S. Patent Application Ser. No. 62/861,186, filed on Jun. 13, 2019. The entire contents of the foregoing are hereby incorporated by reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under grant no. GM118158 awarded by the National Institutes of Health. The Government has certain rights in the invention.

SEQUENCE LISTING

This application contains a Sequence Listing that has been submitted electronically as an XML file named ‘29539-0385003 SL ST26.txt’. The XML file, created on Jul. 10, 2023, is 136,545 bytes in size. The material in the XML file is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

Described herein are engineered human-endogenous virus-like particles (heVLPs) comprising a membrane comprising a phospholipid bilayer on the external side; and a cargo, e.g., a biomolecule and/or chemical cargo, disposed in the core of the heVLP on the inside of the membrane, wherein the heVLP does not comprise a protein from non-human gag or pol, and methods of use thereof for delivery of the cargo to cells.

BACKGROUND

Delivery of cargo such as proteins, nucleic acids, and/or chemicals into the cytosol of living cells has been a significant hurdle in the development of biological therapeutics.

SUMMARY

Described herein are heVLPs that are capable of packaging and delivering DNA, RNA, protein, chemical compounds and/or molecules, and any combination of these four entities into eukaryotic cells. The non-viral heVLP systems described herein have the potential to be simpler, more efficient and safer than conventional, artificially-derived lipid/gold nanoparticles and viral particle-based delivery systems because heVLPs are comprised of human-derived components. The cargo inside may or may not be human derived, but the heVLP is entirely comprised from human and synthetic non-immunogenic components. “Synthetic” components include surface scFv/nanobody/darpin peptides that have been demonstrated to not be immunostimulatory and can be used to enhance targeting and cellular uptake of heVLPs. This means that the exterior surface of the particle lacks components that are significantly immunostimulatory, which should minimize immunogenicity and antibody neutralization of these particles. Excluding cargo, the heVLPs do not contain exogenous viral components inherent to other VLPs and this represents a significant and novel advancement in technology. In addition, heVLPs can utilize (but do not require) chemical-based dimerizers, and heVLPs have the ability to package and deliver cargo molecules including therapeutic or diagnostic agents, including biomolecules and chemicals, e.g., specialty single and/or double-stranded DNA molecules (e.g., plasmid, mini circle, closed-ended linear DNA, AAV DNA, episomes, bacteriophage DNA, homology directed repair templates, etc.), single and/or double-stranded RNA molecules (e.g., single guide RNA, prime editing guide RNA, messenger RNA, transfer RNA, long non-coding RNA, circular RNA, RNA replicon, circular or linear splicing RNA, micro RNA, small interfering RNA, short hairpin RNA, piwi-interacting RNA, toehold switch RNA, RNAs that can be bound by RNA binding proteins, bacteriophage RNA, internal ribosomal entry site containing RNA, etc.), proteins, chemical compounds and/or molecules (e.g., small molecules), and combinations of the above listed cargos (e.g. AAV particles).

The heVLPs described herein are different from conventional retroviral particles, virus-like particles (VLPs), exosomes and other previously described extracellular vesicles that can be loaded with cargo, at least because heVLPs can be produced by a strategic overexpression of human-derived components in human cells, heVLPs have a vast diversity of possible cargos and loading strategies, heVLPs lack a limiting DNA/RNA length constraint, heVLPs lack proteins derived from pol and exogenous gag, and heVLPs have unique mechanisms of cellular entry.

Described herein are compositions and methods for cargo delivery that can be used with a diverse array of protein and nucleic acid molecules, including genome editing, epigenome modulation, transcriptome editing and proteome modulation reagents, that are applicable to many disease therapies.

Thus, provided herein are engineered heVLPs, comprising a membrane comprising a phospholipid bilayer with one or more HERV-derived ENV/glycoprotein(s) (e.g., overexpressed from exogenous sources, such as plasmids or stably integrated transgenes, in heVLP production cells) (e.g., as shown in Table 1) on the external side; and a human endogenous GAG protein, other plasma membrane recruitment domain, and/or biomolecule/chemical cargo disposed in the core of the heVLP on the inside of the membrane, wherein the biomolecule cargo may or may not be fused to a human-endogenous GAG or other plasma membrane recruitment domain (e.g., as shown in Table 6), and the heVLP does not comprise a non-human gag and/or pol protein, do not express gag and/or pol proteins except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome. Human-derived GAG or other plasma membrane recruitment domains fused to biomolecule cargo can be overexpressed from exogenous sources, such as plasmids or stably integrated transgenes, in heVLP production cells.

In some embodiments, the HERV ENV can be truncated or fused to an scFv or other targeting polypeptides.

In some embodiments the HERV GAG can be fused to a plasma membrane recruitment domain (e.g., as shown in Table 6).

In another embodiment, engineered heVLPs comprise a membrane comprising a phospholipid bilayer with one or more HERV-derived ENV/glycoprotein(s) (e.g., overexpressed from exogenous sources, such as plasmids or stably integrated transgenes, in heVLP production cells) (e.g., as shown in Table 1) on the external side; and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6); and, if desired a biomolecule/chemical cargo inside the particle.

Also provided are methods of delivering a cargo to a target cell, e.g., a cell in vivo or in vitro, by contacting the cell with the heVLP of claim 1 comprising the biomolecule and/or chemical as cargo.

In addition, provided herein are methods for producing a heVLP comprising a biomolecular cargo. The methods include providing a cell expressing (e.g., engineered to express or overexpress) one or more HERV-derived envelope proteins (e.g., as shown in Table 1), and a cargo, wherein the cell does not express a gag and/or pol protein, except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome; and maintaining the cell under conditions such that the cells produce heVLPs. In some embodiments, the methods further include harvesting and optionally purifying and/or concentrating the produced heVLPs.

Also provided herein are cells (e.g., isolated cells, preferably mammalian, e.g., human, cells) that express, e.g., that have been induced to overexpress, in combination one or more HERV-derived envelope proteins (e.g., (overexpressed from exogenous sources, such as plasmids or stably integrated transgenes)(e.g., as shown in Table 1), and a cargo fused to a human endogenous GAG or other plasma membrane recruitment domain (e.g., as shown in Table 6), wherein the cell does not express a gag protein except for gag proteins that are encoded in the human genome or gag proteins that are encoded by a consensus sequence that is derived from gag proteins found in the human genome (overexpressed from exogenous sources, such as plasmids or stably integrated transgenes)). In some embodiments, the cells are primary or stable human cell lines, e.g., Human Embryonic Kidney (HEK) 293 cells, HEK293 T cells, or BeWo cells. The cells can be used to produce heVLPs as described herein.

In some embodiments, the methods include using cells that have or have not been manipulated to express any exogenous proteins except for a HERV envelope (e.g., as shown in Table 1), and, if desired, a plasma membrane recruitment domain (e.g., as shown in Table 6). In this embodiment, the “empty” particles that are produced can be loaded with biomolecule or chemical molecule cargo by utilizing nucleofection, lipid, polymer, or CaCl₂ transfection, sonication, freeze thaw, and/or heat shock of purified particles mixed with cargo. In all embodiments, producer cells do not express any human exogenous gag protein. This type of loading allows for cargo to be unmodified by fusions to plasma membrane recruitment domains and represents a significant advancement from previous VLP technology.

In another embodiment, heVLPs that contain cargo are produced and isolated can be loaded with additional biomolecule or chemical molecule cargo by utilizing nucleofection, lipid, polymer, or CaCl₂ transfection, sonication, freeze thaw, incubation at various temperatures, and/or heat shock of purified particles mixed with cargo.

In some embodiments, the cargo is a therapeutic or diagnostic protein or nucleic acid encoding a therapeutic or diagnostic protein.

In some embodiments, the cargo is a chemical compound or molecule.

In some embodiments, the chemical molecule is a trigger for protein-protein dimerization of multimerization, such as the A/C heterodimerizer or rapamycin.

In some embodiments, the chemical compound is a DNA PK inhibitor, such as M3814, NU7026, or NU7441 which potently enhance homology directed repair gene editing.

In some embodiments, the biomolecule cargo is a gene editing reagent.

In some embodiments, the gene editing reagent comprises a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-based genome editing or modulating protein; a nucleic acid encoding a zinc finger (ZF), transcription activator-like effector (TALE), and/or CRISPR-based genome editing or modulating protein; or a riboucleoprotein complex (RNP) comprising a CRISPR-based genome editing or modulating protein.

In some embodiments, the gene editing reagent is selected from the proteins listed in Tables 2, 3, 4 & 5.

In some embodiments, the gene editing reagent comprises a CRISPR-based genome editing or modulating protein, and the heVLP further comprises one or more guide RNAs that bind to and direct the CRISPR-based genome editing or modulating protein to a target sequence.

In some embodiments, the cargo comprises a covalent or non-covalent connection to a human-endogenous GAG or other plasma membrane recruitment domain, preferably as shown in Table 6. Covalent connections, for example, can include direct protein-protein fusions generated from a single reading frame, inteins that can form peptide bonds, other proteins that can form covalent connections at R-groups and/or RNA splicing. Non-covalent connections, for example, can include DNA/DNA, DNA/RNA, and/or RNA/RNA hybrids (nucleic acids base pairing to other nucleic acids via hydrogen-bonding interactions), protein domains that dimerize or multimerize with or without the need for a chemical compound/molecule to induce the protein-protein binding, single chain variable fragments, nanobodies, affibodies, proteins that bind to DNA and/or RNA, proteins with quaternary structural interactions, optogenetic protein domains that can dimerize or multimerize in the presence of certain light wavelengths, and/or naturally reconstituting split proteins.

In some embodiments, the cargo comprises a fusion to a dimerization domain or protein-protein binding domain that may or may not require a molecule to trigger dimerization or protein-protein binding.

In some embodiments, the producer cells are FDA-approved cells lines, allogenic cells, and/or autologous cells derived from a donor.

In some embodiments, the full or active peptide domains of human CD47 may be incorporated in the heVLP surface to reduce immunogenicity.

Examples of AAV proteins included here are AAV REP 52, REP 78, and VP1-3. The capsid site where proteins can be inserted is T138 starting from the VP1 amino acid counting. Dimerization domains could be inserted at this point in the capsid, for instance.

Examples of dimerization domains included here that may or may not need a small molecule inducer are dDZF1, dDZF2, DmrA, DmrB, DmrC, FKBP, FRB, GCN4 scFv, 10×/24×GCN4, GFP nanobody and GFP.

Examples of split inteins included here are Npu DnaE, Cfa, Vma, and Ssp DnaE.

Examples of other split proteins included here that make a covalent bond together are Spy Tag and Spy Catcher.

Examples of RNA binding proteins included here are MS2, Com, and PP7.

Examples of synthetic DNA-binding zinc fingers included here are ZF6/10, ZF8/7, ZF9, MK10, Zinc Finger 268, and Zinc Finger 268/NRE.

Examples of proteins that multimerize as a result of quaternary structure included here are E. coli ferritin, and the other chimeric forms of ferritin.

Examples of optogenetic “light-inducible proteins” included here are Cry2, CIBN, and Lov2-Ja.

Examples of peptides the enhance transduction included here are L17E, Vectofusin, KALA, and the various forms of nisin.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 : Depiction of exemplary T2heVLP/T4heVLP production and transduction for RNP/protein delivery. All heVLP expression constructs are stably integrated in the genome of the producer cell. Construct 1-0 corresponds to the human-endogenous GAG (hGAG). Construct 1-1 corresponds to the human-endogenous GAG or other phospholipid bilayer recruitment domain. 1-2 corresponds to the cargo. 2 corresponds to an optional guide RNA. 1-0, 1-1 and 1-2 are translated in the cytosol where the fusion of 1-1 and 1-2 complexes with guide RNA before it is recruited to the phospholipid bilayer. 3 corresponds to a HERV-derived glycoprotein (hENV). The HERV-derived glycoprotein is expressed as a transmembrane protein on the plasma membrane. hGAG drives budding of cargo-containing heVLPs from the plasma membrane to extracellular space. These particles are purified and are able to fuse with target cells and deliver cargo by interacting with surface receptors at the target cell surface.

FIG. 2 : Depiction of purified heVLPs entering a target cell and delivering cargo to the cytosol. Importantly, the human-endogenous GAG or other phospholipid bilayer recruitment domain allows cargo to enter the target cell nucleus as long as cargo possesses a nuclear localization sequence.

FIG. 3 : Exemplary T1heVLP-delivered spCas9 genome editing in vitro. HEK 293T cells transduced with T1heVLPs containing PLC PH fused to spCas9, hGAGK_(con) fused to spCas9, or human Activity-regulated cytoskeleton-associated protein (hArc) fused to spCas9 targeted to VEGF site #3. heVLPs are pseudotyped with either hENVW (left chart) or hENVFRD (right chart). Gene modification is measured by amplicon sequencing.

FIG. 4 : Depiction of T1heVLP/T3heVLP production. Plasmid DNA constructs involved in the transfection encode cargo, an optional guide RNA, hGAG and a HERV-derived glycoprotein. Plasmids, or other types of DNA molecules, will be distributed throughout the production cell, so constructs located in the nucleus will express heVLP components and cargo, and constructs located near the plasma membrane or endosomes will be encapsulated within budding heVLPs.

FIG. 5 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 6 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo-gag fusion or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 7 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo-PH fusion or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 8 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo-gag/PH fusion or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 9 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C heterodimerizer) either by producer cells expressing cargo and gag fused to DmrA or DmrC or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 10 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C heterodimerizer) either by producer cells expressing cargo and PH fused to DmrA or DmrC or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 11 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C heterodimerizer) either by producer cells expressing cargo and gag/PH fused to DmrA or DmrC or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 12 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and gag fused to an RNA binding protein (RBP), MS2, that binds to its MS2 RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 13 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and PH fused to an RNA binding protein (RBP), MS2, that binds to its RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 14 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and gag/PH fused to an RNA binding protein (RBP), MS2, that binds to its RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 15 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of dimerization molecule (A/C Heterodimerizer) either by producer cells expressing cargo and gag and an RNA binding protein (RBP), MS2, fused to DmrA or DmrC that binds to its RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 16 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of dimerization molecule (A/C Heterodimerizer) either by producer cells expressing cargo and PH and an RNA binding protein (RBP), MS2, fused to DmrA or DmrC that binds to its RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 17 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of dimerization molecule (A/C Heterodimerizer) either by producer cells expressing cargo and gag/PH and an RNA binding protein (RBP), MS2, fused to DmrA or DmrC that binds to its RNA stem loop (MS2 SL) that is complexed with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 18 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and gag fused to a repetitive GCN4 domain that is bound by an scFv that is fused with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 19 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and PH fused to a repetitive GCN4 domain that is bound by an scFv that is fused with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 20 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle either by producer cells expressing cargo and gag/PH fused to a repetitive GCN4 domain that is bound by an scFv that is fused with cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 21 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C Heterodimerizer) by producer cells expressing gag and a repetitive GCN4 domain that are fused to DmrA or DmrC. GCN4 is bound by an scFv that is fused with cargo that is also being expressed in producer cells. Particles could also be loaded by various particle loading methods described herein, such as electroporation.

FIG. 22 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C Heterodimerizer) by producer cells expressing PH and a repetitive GCN4 domain that are fused to DmrA or DmrC. GCN4 is bound by an scFv that is fused with cargo that is also being expressed in producer cells. Particles could also be loaded by various particle loading methods described herein, such as electroporation.

FIG. 23 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo was packaged inside the particle in the presence of a dimerization molecule (A/C Heterodimerizer) by producer cells expressing gag/PH and a repetitive GCN4 domain that are fused to DmrA or DmrC. GCN4 is bound by an scFv that is fused with cargo that is also being expressed in producer cells. Particles could also be loaded by various particle loading methods described herein, such as electroporation.

FIG. 24 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles) was packaged inside the particle either by producer cells expressing cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 25 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles) was packaged inside the particle either by producer cells expressing cargo and gag or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 26 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles) was packaged inside the particle either by producer cells expressing cargo and PH or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 27 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles) was packaged inside the particle either by producer cells expressing cargo and gag/PH or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 28 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer molecule either by producer cells expressing cargo and gag fused to DmrB or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 29 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer molecule either by producer cells expressing cargo and PH fused to DmrB or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 30 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer molecule either by producer cells expressing cargo and gag/PH fused to DmrB or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 31 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer and A/C Heterodimerizer molecules either by producer cells expressing cargo and gag fused to DmrA, DmrB, or DmrC, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 32 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer and A/C Heterodimerizer molecules either by producer cells expressing cargo and PH fused to DmrA, DmrB, or DmrC, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 33 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (AAV particles with DmrB inserted in the Capsid protein, VP2) was packaged inside the particle in the presence of DmrB dimerizer and A/C Heterodimerizer molecules either by producer cells expressing cargo and gag/PH fused to DmrA, DmrB, or DmrC, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 34 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (single-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 35 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag. Cargo (single-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 36 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH. Cargo (single-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 37 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH. Cargo (single-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 38 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 39 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 40 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 41 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 42 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 43 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 44 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 45 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag and a zinc finger protein (ZFP) that will bind a specific sequence in the cargo fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 46 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH and a zinc finger protein (ZFP) that will bind a specific sequence in the cargo fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 47 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH and a zinc finger protein (ZFP) that will bind a specific sequence in the cargo fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA) can be packaged inside the particle by various particle loading methods described herein, such as electroporation.

FIG. 48 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 49 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 50 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH fused to a zinc finger protein (ZFP) that will bind a specific sequence in the cargo. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 51 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag fused to a zinc finger protein (ZFP) fused to DmrA or DmrC that will bind a specific sequence in the cargo in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 52 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and PH fused to a zinc finger protein (ZFP) fused to DmrA or DmrC that will bind a specific sequence in the cargo in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 53 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein and gag/PH fused to a zinc finger protein (ZFP) fused to DmrA or DmrC that will bind a specific sequence in the cargo in the presence of A/C Heterodimerizer molecule. Cargo (double-stranded DNA bound by Cas9 RNP-ZFP fusion) can be packaged inside the particle by various particle loading methods described herein, such as electroporation. Alternatively, the Cas9 RNP-ZFP fusion could be expressed by the producer cells and the particles could be loaded by various particle loading methods described herein, such as electroporation.

FIG. 54 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA) was packaged inside the particle either by producer cells expressing cargo or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 55 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA) was packaged inside the particle either by producer cells expressing cargo and gag or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 56 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA) was packaged inside the particle either by producer cells expressing cargo and PH or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 57 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA) was packaged inside the particle either by producer cells expressing cargo and gag/PH or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 58 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and gag fused to MS2 or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 59 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and PH fused to MS2 or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 60 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and gag/PH fused to MS2 or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 61 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and gag and MS2 fused to DmrA or DmrC in the presence of A/C heterodimerizer, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 62 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and PH and MS2 fused to DmrA or DmrC in the presence of A/C heterodimerizer, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 63 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with MS2 stem loop(s)) was packaged inside the particle either by producer cells expressing cargo and gag/PH and MS2 fused to DmrA or DmrC in the presence of A/C heterodimerizer, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 64 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and gag fused to another RBP or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 65 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and PH fused to another RBP or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 66 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and gag/PH fused to another RBP or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 67 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and gag and another RBP fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 68 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and PH and another RBP fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule, or particles being loaded by various particle loading methods described herein, such as electroporation.

FIG. 69 : Depiction of exemplary heVLP and cargo configuration

This particle was created by producer cells expressing an envelope protein. Cargo (RNA with RBP stem loop(s)) was packaged inside the particle either by producer cells expressing cargo fused to an RBP and gag/PH and another RBP fused to DmrA or DmrC in the presence of A/C Heterodimerizer molecule, or particles being loaded by various particle loading methods described herein, such as electroporation.

DETAILED DESCRIPTION

Therapeutic proteins and nucleic acids hold great promise, but for many of these large biomolecules delivery into cells is a hurdle to clinical development. Genome editing reagents such as zinc finger nucleases (ZFNs) or RNA-guided, enzymatically active/inactive DNA binding proteins such as Cas9 have undergone rapid advancements in terms of specificity and the types of edits that can be executed, but the hurdle of safe in vivo delivery still precludes efficacious gene editing therapies. The following details the characteristics of the heVLP that make it a novel and optimal platform for the delivery of genome editing reagents, and contrasts heVLPs with canonical delivery modalities.

Retroviral particles, such as lentivirus, have been developed to deliver RNA that is reverse transcribed to DNA that may or may not be integrated into genomic DNA. VLPs have been developed that mimic virus particles in their ability to self-assemble, but are not infectious as they lack some of the core viral genes. Both lentiviral and VLP vectors are typically produced by transiently transfecting a producer cell line with plasmids that encode all components necessary to produce lentiviral particles or VLP. One major flaw that we have discovered regarding lentiviral particles and VSVG-based VLPs that are produced by this conventional transient transfection method is that, in addition to their conventional cargo, these particles package and deliver plasmid DNA that was used in the initial transient transfection. This unintended plasmid DNA delivery can be immunogenic and cause undesirable effects, such as plasmid DNA being integrated into genomic DNA. It is important to specify the type of biomolecules and/or chemicals that are to be delivered within particles, and heVLPs have been designed to possess this germane capability.

The heVLPs described herein can deliver DNA only, DNA+RNA+protein, or RNA+protein. Importantly, heVLPs are the first VLP delivery modality that leverages select components from human endogenous retroviruses (HERVs) to create particles for customizable cargo delivery into eukaryotic cells. heVLPs are capable of controlling the form of the cargo (DNA, protein, and/or RNA). All other previously described VLPs and viral particles package and deliver unwanted plasmid DNA (or other types of DNA-based gene expression constructs) introduced into particle producer cells via transient transfection in addition to the intended protein and/or RNA cargo(s).

Another non-obvious aspect of heVLPs is the ENV protein on the surface of the heVLP. The ENV protein is responsible for the ability of heVLPs to efficiently deliver cargo into cells. The majority of retroviral ENV proteins require post-translational modifications in the form of proteolytic cleavage of the intracellular domain (ICD) of the ENV protein in order to activate the fusogenicity of the ENV protein; this is essential for infectivity.¹ The envelope proteins described in Table 1 are all derived from HERVs that are expressed to varying levels in healthy human tissues (or HERV ENV consensus sequences). Some of these sequences possess ICD truncations that have been shown to enhance fusogenicity, but most do not require truncation.

heVLPs do not require exogenous, virally-derived GAG for particle formation because heVLPs utilize human-endogenous GAG proteins from HERVs (or HERV GAG consensus sequences).¹ These HERV GAG proteins enable heVLP formation and are expressed to varying levels in healthy human tissues. Importantly, heVLPs are different from previously described viral particles, VLPs, and extracellular vesicles because heVLPs are composed of a novel combination of HERV ENV and GAG components, and heVLPs lack components from exogenous viruses.^(2,3) Because of the above mentioned design optimizations, heVLPs are particularly suited for delivery of DNA, RNA, protein, or combinations of biomolecules and/or chemicals, such as DNA-encoded or RNP-based genome editing reagents.

Genome editing reagents, especially CRISPR-CAS, zinc finger, and TAL-nuclease-based reagents have the potential to become in vivo therapeutics for the treatment of genetic diseases, but techniques for delivering genome editing reagents into cells are severely limiting or unsafe for patients. Conventional therapeutic monoclonal antibody delivery is successful at utilizing direct injection for proteins. Unfortunately, strategies for direct injection of gene editing proteins, such as Cas9, are hampered by immunogenicity, degradation, ineffective cell specificity, and inability to cross the plasma membrane or escape endosomes/lysosomes.⁴⁻¹⁰ More broad applications of protein therapy and gene editing could be achieved by delivering therapeutic protein cargo to the inside of cells. Cas9, for example, cannot efficiently cross the phospholipid bilayer to enter into cells, and has been shown to have innate and adaptive immunogenic potential.⁴⁻⁸ Therefore, it is not practical or favorable to deliver Cas9 by direct injection or as an external/internal conjugate to lipid, protein or metal-based nanoparticles that have cytotoxic and immunogenic properties and often yield low levels of desired gene modifications.⁹⁻²⁰

Nanoparticles that encapsulate cargo are another delivery strategy that can be used to deliver DNA, protein, RNA and RNPs into cells⁹⁻¹⁸ Nanoparticles can be engineered for cell specificity and can trigger endocytosis and subsequent endosome lysis. However, nanoparticles can have varying levels of immunogenicity due to an artificially-derived vehicle shell.⁹⁻²⁰ Many nanoparticles rely on strong opposing charge distributions to maintain particle structural integrity, and the electrostatics can make it toxic and unfit for many in vivo therapeutic scenarios.⁹ Nanoparticles that deliver RNA have had successes in recent clinical trials, but most have only been used to deliver siRNA or shRNA. Toxicity from such nanoparticles is still a major concern.⁹ Nanoparticles that deliver mRNA coding for genome editing RNPs have also been a recent success, but these create a higher number of off-target effects compared to protein delivery and RNA stability is lower than that of protein.¹⁷ Nanoparticles that deliver genome editing RNPs and DNA have been a significant breakthrough because they can leverage both homology directed repair (HDR) and non-homologous end joining (NHEJ), but exhibit prohibitively low gene modification frequencies in vitro and in vivo, and therefore currently have limited applications in vivo as a gene editing therapeutic.¹⁵

Currently, the clinical standard vehicles for delivering genome editing therapeutics are adeno-associated virus (AAV). Although AAV vectors are a promising delivery modality that can successfully deliver DNA into eukaryotic cells, AAV cannot efficiently package and deliver DNA constructs larger than 4.5 kb and this precludes delivery of many CRISPR-based gene editing reagents that require larger DNA expression constructs. CRISPR-based gene editing reagents can be split into multiple different AAV particles, but this strategy drastically reduces delivery and editing efficiency. Depending on the dose required, AAV and adenoviral vectors can have varying levels of immunogenicity. In addition, inverted-terminal repeats (ITRs) in the AAV DNA construct can promote the formation of spontaneous episomes leading to prolonged expression of genome editing reagents and increased off-target effects. ITRs can also promote the undesired integration of AAV DNA into genomic DNA.²¹⁻²⁴

Recently, VLPs have been utilized to deliver mRNA and protein cargo into the cytosol of cells.^(2,3,25-30) VLPs have emerged as a substitute delivery modality for retroviral particles. VLPs can be designed to lack the ability to integrate retroviral DNA, and to package and deliver protein/RNP/DNA. However, most VLPs, including recently conceived VLPs that deliver genome editing reagents known to date, utilize HIV or other virally-derived gag-pol protein fusions and viral proteases to generate retroviral-like particles.^(25-27,29,30) Secondly, some VLPs containing RGNs also must package and express guide RNAs from a lentiviral DNA transcript.²⁷ Thirdly, some VLPs require a viral protease in order to form functional particles and release genome editing cargo.^(25-27,29,30) Since this viral protease recognizes and cleaves at multiple amino acid motifs, it can cause damage to the protein cargo which could be hazardous for therapeutic applications. Fourthly, most published VLP modalities that deliver genome editing proteins to date exhibit low in vitro and in vivo gene modification efficiencies due to low packaging and transduction efficiency.²⁵⁻²⁷ Fifthly, the complex viral genomes utilized for these VLP components possess multiple reading frames and employ RNA splicing that could result in spurious fusion protein products being delivered.^(25-27,29,30) Sixthly, the presence of reverse transcriptase, integrase, capsid and a virally-derived envelope protein in these VLPs is not ideal for most therapeutic applications because of immunogenicity and off target editing concerns. Lastly, most retroviral particles, such as lentiviral particles, are pseudotyped with VSVG and nearly all described VLPs that deliver genome editing reagents hitherto possess and rely upon VSVG.^(2,3,25-30) We have discovered that VSVG-based particles that are formed by transiently transfecting producer cells package and deliver DNA that was transfected. The current versions of VSVG-based VLPs cannot prevent this inadvertent delivery of DNA and this impedes the use of VLPs in scenarios that necessitate minimal immunogenicity and off target effects.

Extracellular vesicles are another delivery modality that can package and deliver cargo within exosomes and ectosomes.^(31,32) Similar to VLPs, extracellular vesicles are comprised of a phospholipid bilayer from a mammalian cell. Unlike VLPs, extracellular vesicles lack viral components and therefore have limited immunogenicity. Whereas VLPs have a great ability to enter cells due to external fusogenic glycoproteins (VSVG) extracellular vesicles mainly rely on cellular uptake via micropinocytosis and this limits the delivery efficiency of extracellular vesicles.

heVLPs try to leverage the delivery benefits of extracellular vesicles and VLPs. heVLPs are the first VLP modality to eliminate all the potentially harmful exogenous, virally-derived components. heVLP components are known to be involved in extracellular vesicle biogenesis, they are known to possess local immunosuppressive properties, and their expression in healthy human tissues minimizes the chance of eliciting an immune response because of central tolerance.¹ heVLPs are a safer and more effective alternative than previously described VLPs, extracellular vesicles, AAVs and nanoparticles-especially for delivery of genome editing reagents-because heVLPs are comprised of all human-derived components, heVLPs have the ability to deliver DNA+RNP, or RNP alone while other previously described VLPs cannot prevent transient transfection DNA from being unintentionally packaged and delivered, heVLPs can deliver specialty DNA molecules while previously described VLPs, nanoparticles and AAVs cannot or do not, and heVLPs can be produced with cells that have been derived from patients (autologous heVLPs) and other FDA-approved cell lines (allogenic heVLPs) to further reduce the risks of adverse immune reactions. Here, we describe methods and compositions for producing, purifying, and administering heVLPs for in vitro and in vivo applications of genome editing, epigenome modulation, transcriptome editing and proteome modulation. The desired editing outcome depends on the therapeutic context and will require different gene editing reagents. Streptococcus pyogenes Cas9 (spCas9) and acidaminococcus sp. Cas12a (functionalize) are two of the most popular RNA-guided enzymes for editing that leverages NHEJ for introducing stop codons or deletions, or HDR for causing insertions.³⁴⁻³⁶ Cas9-deaminase fusions, also known as base editors, are the current standard for precise editing of a single nucleotide without double stranded DNA cleavage.^(37,38) Importantly, this invention provides a novel way of packaging and delivering reagents for applications of genome editing, epigenome modulation, transcriptome editing and proteome modulation. Importantly, this invention is also the first to address the phenomenon of inadvertent DNA delivery in VLPs and the first to control for the type of biomolecule to be delivered (DNA, RNA, and/or protein) thereby increasing the types of therapeutic in vivo genome modifications that are possible and minimizing deleterious off target effects.

Section 1: heVLP-Mediated Delivery of Cargo Including DNAs, Proteins, Compounds, and RNAs

Conventional VLPs that have been engineered to encapsulate and deliver protein-based cargo commonly fuse cargo to the INT or GAG polyprotein^(25-27,29,30,39,40) After transient transfection of production plasmid DNA constructs, these protein fusions are translated in the cytosol of conventional VLP production cell lines, the gag matrix is acetylated and recruited to the cell membrane, and the gag fusions are encapsulated (transient transfection DNA is also unintentionally encapsulated) within VLPs as VLPs bud off of the membrane into extracellular space.

In contrast, the heVLPs described herein can package protein-based cargo by integrating all production DNA into the genomic DNA of production cell lines. Once cell lines are created, protein delivery heVLPs can be produced in a constitutive or inducible fashion. Proteins are packaged into heVLP by fusing select human-endogenous GAG proteins or other plasma membrane recruitment domains to protein-based cargo (e.g., as shown in Table 6). Human-endogenous GAG proteins and human pleckstrin homology (PH) domains localize to biological membranes. PH domains interact with phosphatidylinositol lipids and proteins within biological membranes, such as PIP2, PIP3, βγ-subunits of GPCRs, and PKC.^(41,42) However, in addition to localizing to phospholipid bilayers, human-endogenous GAG proteins drive budding and particle formation.⁴² This dual functionality of human-endogenous GAG enables packaging of cargo and budding/formation of particles. One such human-endogenous GAG protein used for this purpose is the human Arc protein can be fused to protein-based cargo to recruit cargo to the cytosolic side of the phospholipid bilayer.⁴³ These human-endogenous GAG phospholipid bilayer recruitment domains can be fused to the N-terminus or C-terminus of protein-based cargo via polypeptide linkers of variable length regardless of the location or locations of one or more nuclear localization sequence(s) (NLS) within the cargo. Preferably, the linker between protein-based cargo and the human-endogenous GAG phospholipid bilayer recruitment domain is a polypeptide linker 5-20, e.g., 8-12, e.g., 10, amino acids in length primarily composed of glycines and serines. The human-endogenous GAG or other phospholipid bilayer recruitment domain localizes the cargo to the phospholipid bilayer and this protein cargo is packaged within heVLPs that bud off from the producer cell into extracellular space (FIG. 1 ). In this application, the use of these human-endogenous GAG and other phospholipid bilayer recruitment domains is novel and unique in that these human-endogenous GAG and other proteins can facilitate for localization of cargo to the cytosolic face of the plasma membrane within the heVLP production cells, and they also allow for cargo to localize to the nucleus of heVLP-transduced cells without the utilization of exogenous retroviral GAG or chemical and/or light-based dimerization systems (FIG. 2 ). The heVLP delivery of Cas9, for example, is significantly more efficient with a fusion to a human-endogenous GAG protein compared to a fusion to a PH plasma membrane recruitment domain or no fusion at all (FIG. 3 ).

heVLPs can also package and deliver a combination of DNA and RNA if heVLPs are produced via transient transfection of a production cell line. DNA that is transfected into cells will possess size-dependent mobility such that a fraction of the transfected DNA will remain in the cytosol while another fraction of the transfected DNA will localize to the nucleus.⁴⁴⁻⁴⁶ One fraction of the transfected DNA in the nucleus will expressed components needed to create heVLPs and the other fraction in the cytosol/near the plasma membrane will be encapsulated and delivered in heVLPs (FIG. 4 ).

heVLP “Cargo” as used herein can refer to a one or more of chemicals, e.g., small molecule compounds, combination of DNA, RNA, and protein, a combination of RNA and protein, a combination of DNA and protein, or protein, e.g., for therapeutic or diagnostic use, or for the applications of genome editing, epigenome modulation, and/or transcriptome modulation. In addition, endogenous RNA and protein from the producer cells get packaged and/or incorporated into heVLPs. In order to simplify these distinctions, a combination of exogenous DNA, exogenous RNA, and protein (exogenous and/or endogenous protein) will be referred to as type 1 cargo (T1heVLPs), exogenous RNA and protein (exogenous and/or endogenous protein) will be referred to as type 2 cargo (T2heVLPs), a combination of exogenous DNA and proteins (exogenous and/or endogenous protein) will be referred to as type 3 cargo (T3heVLPs), proteins (exogenous and/or endogenous protein) will be referred to as type 4 cargo (T4heVLPs). Therefore, T1 contains DNA, RNA, +/−exogenous protein, T2 contains RNA+/−exogenous protein, T3 contains DNA+/−exogenous protein, and T4 is a particle with or without exogenous protein cargo. Hence, T4 without exogenous protein is considered an “empty particle” because there is no “exogenous cargo.” “Exogenous cargo” is cargo not endogenous to the producer cells that can be packaged and/or incorporated into heVLPs. In addition, T1-T4heVLPs can package exogenous chemical molecules in addition to the types of cargoes present in T1-T4heVLPs. RNA in this context, for example, could be single guide RNA (sgRNA), Clustered Regularly Interspaced Palindromic Repeat (CRISPR) RNA (crRNA), and/or mRNA coding for cargo.

As used herein, “small molecules” refers to small organic or inorganic molecules of molecular weight below about 3,000 Daltons. In general, small molecules useful for the invention have a molecular weight of less than 3,000 Daltons (Da). The small molecules can be, e.g., from at least about 100 Da to about 3,000 Da (e.g., between about 100 to about 3,000 Da, about 100 to about 2500 Da, about 100 to about 2,000 Da, about 100 to about 1,750 Da, about 100 to about 1,500 Da, about 100 to about 1,250 Da, about 100 to about 1,000 Da, about 100 to about 750 Da, about 100 to about 500 Da, about 200 to about 1500, about 500 to about 1000, about 300 to about 1000 Da, or about 100 to about 250 Da).

The cargo is limited by the diameter of the particles, e.g., which in some embodiments range from 150 nm to 500 nm.

Cargo developed for applications of genome editing also includes nucleases and base editors. Nucleases include FokI and AcuI ZFNs and Transcription activator-like effector nucleases (TALENs) and CRISPR based nucleases or a functional derivative thereof (e.g., as shown in Table 2) (ZFNs are described, for example, in United States Patent Publications 20030232410; 20050208489; 20050026157; 20050064474; 20060188987; 20060063231; and International Publication WO 07/014275) (TALENs are described, for example, in United States Patent Publication U.S. Pat. No. 9,393,257B2; and International Publication WO2014134412A1) (CRISPR based nucleases are described, for example, in United States Patent Publications U.S. Pat. No. 8,697,359B1; US20180208976A1; and International Publications WO2014093661A2; WO2017184786A8).³⁴⁻³⁶ Base editors that are described by this work include any CRISPR based nuclease orthologs (wt, nickase, or catalytically inactive (CI)), e.g., as shown in Table 2, fused at the N-terminus to a deaminase or a functional derivative thereof (e.g., as shown in Table 3) with or without a fusion at the C-terminus to one or multiple uracil glycosylase inhibitors (UGIs) using polypeptide linkers of variable length (Base editors are described, for example, in United States Patent Publications US20150166982A1; US20180312825A1; U.S. Ser. No. 10/113,163B2; and International Publications WO2015089406A1; WO2018218188A2; WO2017070632A2; WO2018027078A8; WO2018165629A1).^(37,38) In addition, prime editors are also compatible with heVLP delivery modalities (Prime editors are described, for example, in Anzalone et al., Nature. 2019 December; 576(7785):149-157).

sgRNAs complex with genome editing reagents during the packaging process and are co-delivered within heVLPs. To date, this concept has been validated in vitro by experiments that demonstrate the T2heVLP delivery of RGN RNP for the purposes of site specific editing of an endogenous site (FIG. 3 ). For example, T2heVLPs have been used to deliver Cas9 RNP to HEK 293T cells for the purposes of editing endogenous VEGF site #3 (FIG. 3 ).

Cargo designed for the purposes of epigenome modulation includes the CI CRISPR based nucleases, zinc fingers (ZFs) and TALEs fused to an epigenome modulator or combination of epigenome modulators or a functional derivative thereof connected together by one or more variable length polypeptide linkers (Tables 2 & 4). T1-T4 cargo designed for the purposes of transcriptome editing includes CRISPR based nucleases or any functional derivatives thereof in Table 5 or CI CRISPR based nucleases or any functional derivatives thereof in Table 5 fused to deaminases in Table 3 by one or more variable length polypeptide linkers.

The cargo can also include any therapeutically or diagnostically useful protein, DNA, RNP, or combination of DNA, protein and/or RNP. See, e.g., WO2014005219; U.S. Ser. No. 10/137,206; US20180339166; U.S. Pat. No. 5,892,020A; EP2134841B1; WO2007020965A1. For example, cargo encoding or composed of nuclease or base editor proteins or RNPs or derivatives thereof can be delivered to retinal cells for the purposes of correcting a splice site defect responsible for Leber Congenital Amaurosis type 10. In the mammalian inner ear, heVLP delivery of base editing reagents or HDR promoting cargo to sensory cells such as cochlear supporting cells and hair cells for the purposes of editing β-catenin (β-catenin Ser 33 edited to Tyr, Pro, or Cys) in order to better stabilize β-catenin could help reverse hearing loss.

In another application, heVLP delivery of RNA editing reagents or proteome perturbing reagents could cause a transitory reduction in cellular levels of one or more specific proteins of interest (potentially at a systemic level, in a specific organ or a specific subset of cells, such as a tumor), and this could create a therapeutically actionable window when secondary drug(s) could be administered (this secondary drug is more effective in the absence of the protein of interest or in the presence of lower levels of the protein of interest). For example, heVLP delivery of RNA editing reagents or proteome perturbing reagents could trigger targeted degradation of MAPK and PI3K/AKT proteins and related mRNAs in vemurafenib/dabrafenib-resistant BRAF-driven tumor cells, and this could open a window for the administration of vemurafenib/dabrafenib because BRAF inhibitor resistance is temporarily abolished (resistance mechanisms based in the MAPK/PI3K/AKT pathways are temporarily downregulated by heVLP cargo). This example is especially pertinent when combined with heVLPs that are antigen inducible and therefore specific for tumor cells.

In another application, heVLPs could deliver Yamanaka factors Oct3/4, Sox2, Klf4, and c-Myc to human or mouse fibroblasts in order to generate induced pluripotent stem cells.

In another application, heVLPs could deliver dominant-negative forms of proteins in order to elicit a therapeutic effect.

heVLPs that are antigen-specific could be targeted to cancer cells in order to deliver proapoptotic proteins BIM, BID, PUMA, NOXA, BAD, BIK, BAX, BAK and/or HRK in order to trigger apoptosis of cancer cells.

90% of pancreatic cancer patients present with unresectable disease. Around 30% of patients with unresectable pancreatic tumors will die from local disease progression, so it is desirable to treat locally advanced pancreatic tumors with ablative radiation, but the intestinal tract cannot tolerate high doses of radiation needed to cause tumor ablation. Selective radioprotection of the intestinal tract enables ablative radiation therapy of pancreatic tumors while minimizing damage done to the surrounding gastrointestinal tract. To this end, heVLPs could be loaded with dCas9 fused to the transcriptional repressor KRAB and guide RNA targeting EGLN. EGLN inhibition has been shown to significantly reduce gastrointestinal toxicity from ablative radiation treatments because it causes selective radioprotection of the gastrointestinal tract but not the pancreatic tumor.⁴⁷

Unbound steroid receptors reside in the cytosol. After binding to ligands, these receptors will translocate to the nucleus and initiate transcription of response genes. heVLPs could deliver single chain variable fragment (scFv) antibodies to the cytosol of cells that bind to and disrupt cytosolic steroid receptors. For example, the scFv could bind to the glucocorticoid receptor and prevent it from binding dexamethasone, and this would prevent transcription of response genes, such as metallothionein IE which has been linked to tumorigenesis.⁴⁸

heVLPs can be indicated for treatments that involve targeted disruption of proteins. For example, heVLPs can be utilized for targeting and disrupting proteins in the cytosol of cells by delivering antibodies/scFvs to the cytosol of cells. Classically, delivery of antibodies through the plasma membrane to the cytosol of cells has been notoriously difficult and inefficient. This mode of protein inhibition is similar to how a targeted small molecule binds to and disrupts proteins in the cytosol and could be useful for the treatment of a diverse array of diseases.⁴⁹⁻⁵¹

In addition, the targeting of targeted small molecules is limited to proteins of a certain size that contain binding pockets which are relevant to catalytic function or protein-protein interactions. scFvs are not hampered by these limitations because scFvs can be generated that bind to many different moieties of a protein in order to disrupt catalysis and interactions with other proteins. For example, RAS oncoproteins are implicated across a multitude of cancer subtypes, and RAS is one of the most frequently observed oncogenes in cancer. For instance, the International Cancer Genome Consortium found KRAS to be mutated in 95% of their Pancreatic Adenocarcinoma samples. RAS isoforms are known to activate a variety of pathways that are dysregulated in human cancers, like the PI3K and MAPK pathways. Despite the aberrant roles RAS plays in cancer, no efficacious pharmacologic direct or indirect small molecule inhibitors of RAS have been developed and approved for clinical use. One strategy for targeting RAS could be heVLPs that can deliver specifically to cancer cells scFvs that bind to and disrupt the function of multiple RAS isoforms.⁴⁹⁻⁵¹

FIGS. 5-69 provide exemplary heVLP configurations and non-limiting examples of cargo molecules.

Section 2: heVLP Composition, Production, Purification and Applications

heVLPs are produced from producer cell lines that are either transiently transfected with at least one plasmid or stably expressing constructs that have been integrated into the producer cell line genomic DNA. In some embodiments, for T1 and T3heVLPs, if a single plasmid is used in the transfection, it should comprise sequences encoding one or more HERV-derived glycoproteins (e.g., as shown in Table 1), one or more HERV-derived GAG proteins, cargo (e.g., a therapeutic protein or a gene editing reagent such as a zinc finger, transcription activator-like effector (TALE), and/or CRISPR-based genome editing/modulating protein and/or RNP such as those found in Tables 2, 3, 4 & 5) with a fusion to a human-endogenous GAG or other plasma membrane recruitment domain (e.g., as shown in Table 6), and a guide RNA, if necessary. Preferably, two to three plasmids are used in the transfection. These two to three plasmids can include the following (any two or more can be combined in a single plasmid):

-   -   1. A plasmid comprising sequences encoding a therapeutic protein         or a genome editing reagent, with a fusion to a human-endogenous         GAG or other plasma membrane recruitment domain.     -   2. A plasmid comprising one or more HERV-derived glycoproteins         (e.g., as listed in Table 1).     -   3. A plasmid comprising one or more HERV-derived GAG proteins.     -   4. If the genome editing reagent from plasmid 1 requires one or         more guide RNAs, a plasmid comprising one or more guide RNAs         apposite for the genome editing reagent in plasmid 1.

If it is desired to deliver a type of DNA molecule other than plasmid(s), the above-mentioned transfection can be performed with double-stranded closed-end linear DNA, episome, mini circle, double-stranded oligonucleotide and/or other specialty DNA molecules. Alternatively, for T2 and T4heVLPs, the producer cell line can be made to stably express the constructs (1 through 3) described in the transfection above.

The plasmids, or other types of specialty DNA molecules described above, will also preferably include other elements to drive expression or translation of the encoded sequences, e.g., a promoter sequence; an enhancer sequence, e.g., 5′ untranslated region (UTR) or a 3′ UTR; a polyadenylation site; an insulator sequence; or another sequence that increases or controls expression (e.g., an inducible promoter element).

Preferably, appropriate producer cell lines are primary or stable human cell lines refractory to the effects of transfection reagents and fusogenic effects due glycoproteins. Examples of appropriate cell lines include Human Embryonic Kidney (HEK) 293 cells, HEK293 T/17 SF cells kidney-derived Phoenix-AMPHO cells, and placenta-derived BeWo cells. For example, such cells could be selected for their ability to grow as adherent cells, or suspension cells. In some embodiments, the producer cells can be cultured in classical DMEM under serum conditions, serum-free conditions, or exosome-free serum conditions. T1 and T3heVLPs can be produced from cells that have been derived from patients (autologous heVLPs) and other FDA-approved cell lines (allogenic heVLPs) as long as these cells can be transfected with DNA constructs that encode the aforementioned heVLP production components by various techniques known in the art.

In addition, if it is desirable, more than one genome editing reagent can be included in the transfection. The DNA constructs can be designed to overexpress proteins in the producer cell lines. The plasmid backbones, for example, used in the transfection can be familiar to those skilled in the art, such as the pCDNA3 backbone that employs the CMV promoter for RNA polymerase II transcripts or the U6 promoter for RNA polymerase III transcripts. Various techniques known in the art may be employed for introducing nucleic acid molecules into producer cells. Such techniques include chemical-facilitated transfection using compounds such as calcium phosphate, cationic lipids, cationic polymers, liposome-mediated transfection, such as cationic liposome like LIPOFECTAMINE (LIPOFECTAMINE 2000 or 3000 and TranslT-X2), polyethyleneimine, non-chemical methods such as electroporation, particle bombardment, or microinjection.

A human producer cell line that stably expresses the necessary heVLP components in a constitutive and/or inducible fashion can be used for production of T2 and T4heVLPs. T2 and T4heVLPs can be produced from cells that have been derived from patients (autologous heVLPs) and other FDA-approved cell lines (allogenic heVLPs) if these cells have been converted into stable cell lines that express the aforementioned heVLP components.

Also provided herein are the producer cells themselves.

In some embodiments, in order for efficient recruitment of cargo into heVLPs, the cargo comprises a covalent or non-covalent connection to a human-endogenous GAG or other plasma membrane recruitment domain, preferably as shown in Table 6. Covalent connections, for example, can include direct protein-protein fusions generated from a single reading frame, inteins that can form peptide bonds, other proteins that can form covalent connections at R-groups and/or RNA splicing.⁵²⁻⁵⁴ Non-covalent connections, for example, can include DNA/DNA, DNA/RNA, and/or RNA/RNA hybrids (nucleic acids base pairing to other nucleic acids via hydrogen-bonding interactions), protein domains that dimerize or multimerize with or without the need for a chemical compound/molecule to induce the protein-protein binding (such as DmrA/DmrB/DmrC (Takara Bio), FKBP/FRB,⁵⁵ dDZFs,⁵⁶ and Leucine zippers⁵⁷), single chain variable fragments,⁵⁸ nanobodies,⁵⁹ affibodies,⁶⁰ proteins that bind to DNA and/or RNA, proteins with quaternary structural interactions, optogenetic protein domains that can dimerize or multimerize in the presence of certain light wavelengths,⁶¹ and/or naturally reconstituting split proteins.⁶²

In some embodiments, the cargo comprises a fusion to a dimerization domain or protein-protein binding domain that may or may not require a molecule to trigger dimerization or protein-protein binding.

In some embodiments, the producer cells are FDA-approved cells lines, allogenic cells, and/or autologous cells derived from a donor.

In some embodiments, the full or active peptide domains of human CD47 may be incorporated in the heVLP surface to reduce immunogenicity.

Examples of AAV proteins included here are AAV REP 52, REP 78, and VP1-3. The capsid site where proteins can be inserted is T138 starting from the VP1 amino acid counting.⁶³ Dimerization domains could be inserted at this point in the capsid, for instance.

Examples of dimerization domains included here that may or may not need a small molecule inducer are dDZF1,⁵⁶ dDZF2,⁵⁶ DmrA (Takara Bio), DmrB (Takara Bio), DmrC (Takara Bio), FKBP,⁵⁵ FRB,⁵⁵ GCN4 scFv,⁵⁸ 10×/24×GCN4,⁵⁸ GFP nanobody⁵⁹ and GFP.⁶⁴

Examples of split inteins included here are Npu DnaE, Cfa, Vma, and Ssp DnaE.⁵²

Examples of other split proteins included here that make a covalent bond together are Spy Tag and Spy Catcher.⁵³

Examples of RNA binding proteins included here are MS2, Com, and PP7.⁶⁵ Examples of synthetic DNA-binding zinc fingers included here are ZF6/10, ZF8/7, ZF9, MK10, Zinc Finger 268, and Zinc Finger 268/NRE.^(66,67)

Examples of proteins that multimerize as a result of quaternary structure included here are E. coli ferritin, and the other chimeric forms of ferritin.^(68,69)

Examples of optogenetic “light-inducible proteins” included here are Cry2, CIBN, and Lov2-Ja.₆₁

Examples of peptides the enhance transduction included here are L17E,⁷⁰ Vectofusin-1 (Miltenyi Biotec), KALA,⁷¹ and the various forms of nisin.⁷²

In another embodiment, T1-T4 heVLPs that are produced and isolated can be loaded with biomolecule or chemical molecule cargo by utilizing nucleofection, lipid, polymer, or CaChtransfection, sonication, freeze thaw, incubation at various temperatures, and/or heat shock of purified particles mixed with cargo. These techniques are adapted from techniques employed to load cargo into exosomes for therapeutic or research applications.⁷³⁻⁷⁵ For example, 100 ug of heVLPs can be resuspended in 200-450 ul of 50 mM trehalose in PBS, mixed with cargo at a desired concentration, and electroporated (GenePulser II Electroporation System with capacitance extender, Bio-Rad, Hercules, CA, USA) in a 0.4 cm cuvette at 0.200 kV and 125 uF.

Production of Cargo-Loaded heVLPs and Compositions

Preferably heVLPs are harvested from cell culture medium supernatant 36-48 hours post-transfection, or when heVLPs are at the maximum concentration in the medium of the producer cells (the producer cells are expelling particles into the media and at some point in time, the particle concentration in the media will be optimal for harvesting the particles). Supernatant can be purified by any known methods in the art, such as centrifugation, ultracentrifugation, precipitation, ultrafiltration, and/or chromatography. In some embodiments, the supernatant is first filtered, e.g., to remove particles larger than 1 μm, e.g., through 0.45 pore size polyvinylidene fluoride hydrophilic membrane (Millipore Millex-HV) or 0.8 μm pore size mixed cellulose esters hydrophilic membrane (Millipore Millex-AA). After filtration, the supernatant can be further purified and concentrated, e.g., using ultracentrifugation, e.g., at a speed of 80,000 to 100,000×g at a temperature between 1° C. and 5° C. for 1 to 2 hours, or at a speed of 8,000 to 15,000 g at a temperature between 1° C. and 5° C. for 10 to 16 hours. After this centrifugation step, the heVLPs are concentrated in the form of a centrifugate (pellet), which can be resuspended to a desired concentration, mixed with transduction-enhancing reagents, subjected to a buffer exchange, or used as is. In some embodiments, heVLP-containing supernatant can be filtered, precipitated, centrifuged and resuspended to a concentrated solution. For example, polyethylene glycol (PEG), e.g., PEG 8000, or antibody-bead conjugates that bind to heVLP surface proteins or membrane components can be used to precipitate particles. Purified particles are stable and can be stored at 4° C. for up to a week or −80° C. for years without losing appreciable activity.

Preferably, heVLPs are resuspended or undergo buffer exchange so that particles are suspended in an appropriate carrier. In some embodiments, buffer exchange can be performed by ultrafiltration (Sartorius Vivaspin 500 MWCO 100,000). An exemplary appropriate carrier for heVLPs to be used for in vitro applications would preferably be a cell culture medium that is suitable for the cells that are to be transduced by heVLPs. Transduction-enhancing reagents that can be mixed into the purified and concentrated heVLP solution for in vitro applications include reagents known by those familiar with the art (Miltenyl Biotec Vectofusin-1, Millipore Polybrene, Takara Retronectin, Sigma Protamine Sulfate, and the like). After heVLPs in an appropriate carrier are applied to the cells to be transduced, transduction efficiency can be further increased by centrifugation. Preferably, the plate containing heVLPs applied to cells can be centrifuged at a speed of 1,150 g at room temperature for 30 minutes. After centrifugation, cells are returned into the appropriate cell culture incubator (humidified incubator at 37° C. with 5% CO₂).

An appropriate carrier for heVLPs to be administered to a mammal, especially a human, would preferably be a pharmaceutically acceptable composition. A “pharmaceutically acceptable composition” refers to a non-toxic semisolid, liquid, or aerosolized filler, diluent, encapsulating material, colloidal suspension or formulation auxiliary of any type. Preferably, this composition is suitable for injection. These may be in particular isotonic, sterile, saline solutions (monosodium or disodium phosphate, sodium, potassium, calcium or magnesium chloride and and similar solutions or mixtures of such salts), or dry, especially freeze-dried compositions which upon addition, depending on the case, of sterilized water or physiological saline, permit the constitution of injectable solutions. Another appropriate pharmaceutical form would be aerosolized particles for administration by intranasal inhalation or intratracheal intubation.

The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or suspensions. The solution or suspension may comprise additives which are compatible with heVLPs and do not prevent heVLP entry into target cells. In all cases, the form must be sterile and must be fluid to the extent that the form can be administered with a syringe. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. An example of an appropriate solution is a buffer, such as phosphate buffered saline.

Methods of formulating suitable pharmaceutical compositions are known in the art, see, e.g., Remington: The Science and Practice of Pharmacy, 21st ed., 2005; and the books in the series Drugs and the Pharmaceutical Sciences: a Series of Textbooks and Monographs (Dekker, NY). For example, solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying, which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

The compositions comprising cargo-loaded heVLPs can be included in a container, pack, or dispenser together with instructions for administration.

EXAMPLES

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

Methods

heVLP particles were produced by HEK293T cells using polyethylenimine (PEI) based transfection of plasmids. PEI is Polyethylenimine 25 kD linear (Polysciences #23966-2). To make a stock ‘PEI MAX’ solution, 1 g of PEI was added to 1 L endotoxin-free dH₂O that was previously heated to −80° C. and cooled to room temperature. This mixture was neutralized to pH 7.1 by addition of 10N NaOH and filter sterilized with 0.22 μm polyethersulfone (PES). PEI MAX is stored at −20° C.

HEK293T cells were split to reach a confluency of 70%-90% at time of transfection and are cultured in 10% FBS DMEM media. Cargo vectors, such as one encoding a CMV promoter driving expression of a hPLC61 PH fusion to codon optimized Cas9 were co-transfected with a U6 promoter-sgRNA encoding plasmid, a hERVK_(con)GAG (hGAGK_(con)) encoding plasmid, and a hENVW (Syncytin-1) encoding plasmid. Transfection reactions were assembled in reduced serum media (Opti-MEM; GIBCO #31985-070). For heVLP particle production on 10 cm plates, 5 μg PH-Cas9 expressing plasmid, 5 μg sgRNA-expression plasmid, 5 μg hERVK_(con)GAG expression plasmid, and 5 μg Syncytin-1 expression plasmid were mixed in 1 mL Opti-MEM, followed by addition of 27.5 μl PEI MAX. After 20-30 min incubation at room temperature, the transfection reactions were dispersed dropwise over the HEK293T cells.

heVLPs were harvested at 48-72 hours post-transfection. heVLP supernatants were filtered using 0.8 lam pore size mixed cellulose esters membrane filters and transferred to polypropylene Beckman ultracentrifuge tubes that are used with the SW28 rotor (Beckman Coulter #326823). Each ultracentrifuge tube is filled with heVLP-containing supernatant from 3 10 cm plates to reach an approximate final volume of 35-37.5 ml. heVLP supernatant underwent ultracentrifugation at approximately 100,000×g, or 25,000 rpm, at 4° C. for 2 hours. After ultracentrifugation, supernatants were decanted and heVLP pellets resuspended in DMEM 10% FBS media such that they are now approximately 1,000 times more concentrated than they were before ultracentrifugation. heVLPs were added dropwise to cells that were seeded in a 24-well plate 24 hours prior to transduction. Polybrene (5-10 μg/mL in cell culture medium; Sigma-Aldrich #TR-1003-G) was supplemented to enhance transduction efficiency, if necessary. Vectofusin-1 (10 μg/mL in cell culture medium, Miltenyi Biotec #130-111-163) was supplemented to enhance transduction efficiency, if necessary. Immediately following the addition of heVLPs, the 24-well plate was centrifuged at 1,150×g for 30 min at room temperature to enhance transduction efficiency, if necessary.

Example 1

HEK 293T cells were transduced with T1heVLPs containing PLC PH fused to spCas9, hGAGK_(con) fused to spCas9, or hArc fused to spCas9 targeted to VEGF site #3. T1heVLPs were pseudotyped with either hENVW (left chart) or hENVFRD (right chart). Gene modification was measured by amplicon sequencing. Particle purification and concentration was performed by PVDF filtration and ultracentrifugation at 100,000×g for 2 hours. Results are shown in FIG. 3 . Importantly, if HERV-derived GAG (hGAGK_(con)) was not overexpressed by itself in producer cells, then efficient delivery was not achieved.

TABLE 1 Position in sequence entry # HERV envelope Gene name Accession no. (a) 1. hENVH1 envH/p62 AJ289709.1 6313-8067 (+) 2. hENVH2 envH/p60 AJ289710.2 5393-7084 (+) 3. hENVH3 envH/p59 AJ289711.1 5204-6871 (+) 4. hENVK1 envK1 AC074261.3 93508-95604 (+) 5. hENVK2 envK2/HML-2.HOM AC072054.10 30365-32464 (−) 6. hENVK3 envK3/C19 Y17833.1 5581-7680 (+) 7. hENVK4 envK4/K109 AF164615.1 6412-8508 (+) 8. hENVK5 envK5/K113 AY037928.1 6451-8550 (+) 9. hENVK6 envK6/K115 AY037929.1 6442-8541 (+) 10. hENVT envT AC078899.1 154738-156618 (+) 11. hENVW Syncytin-1 AC000064.1 35879-37495 (+) 12. hENVFRD Syncytin-2 AL136139.6 21355-22972 (−) 13. hENVR erv-3 AC073210.8 54963-56978 (−) 14. hENVR(b) envRb AC093488.1 78681-80225 (+) 15. hENVF(c)2 envFc2 AC016222.4 85216-86963 (+) 16. hENVF(c)1 envFc1 AL354685.2 46744-48717 (−) *17. hENVK_(con) N/A N/A N/A (a) ‘+’ and ‘−’ refer to the orientation within the sequence entry *hENVK_(con) is a consensus sequence derived from ten proviral ENV sequences. The ENV sequences used to derive this consensus ENV sequence are from the following HERVs: HERV-K113, HERV-K101, HERV-K102, HERV-K104, HERV-K107, HERV-K108, HERV-K109, HERV-K115, HERV- K11p22, and HERV-K12q13.

TABLE 2 Exemplary Potential Cas9 and Cas12a orthologs DNA-binding Cas ortholog Enzyme class Nickase mutation CI mutations SpCas9 Type II-A D10A D10A, H840A SaCas9 Type II-A D10A D10A, CjCas9 Type II-C D8A D8A, NmeCas9 Type II-C D16A D16A, H588A asCas12a Type II-C D908A, E993A lbCas12a Type II-C D832A, E925A Nickase mutation residues represents a position of the enzyme either known to be required for catalytic activity of the conserved RuvC nuclease domain or predicted to be required for this catalytic activity based on sequence alignment to CjCas9 where structural information is lacking (* indicates which proteins lack sufficient structural information). All positional information refers to the wild-type protein sequences acquired from uniprot.org.

TABLE 3 Exemplary Deaminase domains and their substrate sequence preferences. Deaminase Nucleotide sequence preference hAID 5′-WRC rAPOBEC1* 5′-TC ≥ CC ≥ AC > GC mAPOBEC3 5′-TYC hAPOBEC3A 5′-TCG hAPOBEC3B 5′-TCR > TCT hAPOBEC3C 5′-WYC hAPOBEC3F 5′-TTC hAPOBEC3G 5′-CCC hAPOBEC3H 5′-TTCA~TTCT~TTCG > ACCCA > TGCA ecTadA hAdar1 hAdar2 Nucleotide positions that are poorly specified or are permissive of two or more nucleotides are annotated according to IUPAC codes, where W = A or T, R = A or G, and Y = C or T.

TABLE 4 Exemplary Epigenetic modulator domains. Epigenetic modulator Epigenetic modulation VP16 transcriptional activation VP64 transcriptional activation P65 transcriptional activation RTA transcriptional activation KRAB transcriptional repression MeCP2 transcriptional repression Tet1 Methylation Dnmt3a Methylation

TABLE 5 Exemplary CRISPR based RNA-guided RNA binding enzymes RNA-binding Cas ortholog Enzyme class LshCas13a Type-VI LwaCas13a Type-VI PspCas13b Type-VI RfxCas13d Type-VI

TABLE 6 Plasma membrane recruitment domains described in this work. # Plasma membrane recruitment domain Substitution(s) 1. Pleckstrin homology domain of human phospholipase Cδ1 (hPLCδ1) 2. Pleckstrin homology domain of human Akt1 3. Mutant Pleckstrin homology domain of E17K human Akt1 4. hArc *5. hGAGK_(con) 6. Pleckstrin homology domain of human 3- phosphoinositide-dependent protein kinase 1 (hPDPK1) 7. Human CD9 8. Human CD47 9. Human CD63 10. Human CD81 *hGAGK_(con) is a consensus sequence derived from ten proviral GAG sequences. The GAG sequences used to derive this consensus GAG sequence are from the following HERVs: HERV-K113, HERV-K101, HERV-K102, HERV-K104, HERV-K107, HERV-K108, HERV-K109, HERV-K115, HERV- K11p22, and HERV-K12q13.

Relevant Protein Sequences: Homo sapiens: Arc MELDHRTSGGLHAYPGPRGGQVAKPNVILQIGKCRAEMLEHVRRTHRHLLAEVSK QVERELKGLHRSVGKLESNLDGYVPTSDSQRWKKSIKACLCRCQETIANLERWVK REMHVWREVFYRLERWADRLESTGGKYPVGSESARHTVSVGVGGPESYCHEAD GYDYTVSPYAITPPPAAGELPGQEPAEAQQYQPWVPGEDGQPSPGVDTQIFEDPR EFLSHLEEYLRQVGGSEEYWLSQIQNHMNGPAKKWWEFKQGSVKNWVEFKKEFL QYSEGTLSREAIQRELDLPQKQGEPLDQFLWRKRDLYQTLYVDADEEEIIQYVVGTL QPKLKRFLRHPLPKTLEQLIQRGMEVQDDLEQAAEPAGPHLPVEDEAETLTPAPNS ESVASDRTQPE (SEQ ID NO: 1) >AJ289709.1 Human endogenous retrovirus H HERV-H/env62 HERV_H/ENV_62- hENVH1: MIFAGKAPSNTSTLMKFYSLLLYSLLFSFPFLCHPLPLPSYLHHTINLTHSLLAASNPS LVNNCWLCISLSSSAYTAVPAVQTDWATSPISLHLRTSFNSPHLYPPEELIYFLDRSS KTSPDISHQQAAALLRTYLKNLSPYINSTPPIFGPLTTQTTIPVAAPLCISWQRPTGIPL GNLSPSRCSFTLHLRSPTTNINETIGAFQLHITDKPSINTDKLKNISSNYCLGRHLPCI SLHPWLSSPCSSDSPPRPSSCLLIPSPENNSERLLVDTRRFLIHHENRTFPSTQLPH QSPLQPLTAAALAGSLGVWVQDTPFSTPSHLFTLHLQFCLAQGLFFLCGSSTYMCL PANWTGTCTLVFLTPKIQFANGTEELPVPLMTPTQQKRVIPLIPLMVGLGLSASTVAL GTGIAGISTSVMTFRSLSNDFSASITDISQTLSVLQAQVDSLAAVVLQNRRGLDLLTA EKGGLCIFLNEECCFYLNQSGLVYDNIKKLKDRAQKLANQASNYAEPPWALSNWMS WVLPIVSPLIPIFLLLLFGPCIFRLVSQFIQNRIQAITNHSIRQMFLLTSPQYHPLPQDLP SA (SEQ ID NO: 2) >AJ289710.2 Human endogenous retrovirus H HERV-H/env60- HERV_H_ENV_60-hENVH2: MIFAGRASSNTSTLMKFYSLLLYSLLFSFPILCHPLPLPSYLHHTINLTHSLLAVSNPS LAKNCWLCISLPSSAYPAVPALQTDWGTSPVSPHLRTSFNSPHLYPPEKLIYFLDRS SKTSPDISHQQAAALLCTYLKNLSPYINSTPPTFGPLTTQTTIPVAAPLCISRQRPTGI PLGNLSPSRCSFTLHLRSPTTHITETNGAFQLHITDKPSINTDKLKNVSSNYCLGRHL SCISLHPWLFSPCSSDSPPRPSSCLLIPSPKNNSESLLVDAQRFLIYHENRTSPSTQL PHQSPLQPLTAAPLGGSLRVWVQDTPFSTPSHLFTLHLQFCLVQSLFFLCGSSTYM CLPANWTGTCTLVFLTSKIQFANGTEELPVPLMTPTRQKRVIPLIPLMVGLGLSASTV ALGTGIAGISTSVTTFRILSNDFSASITDISQTLSGLQAQVDSSAAVVLQNRQGLDLLT AEKGGLCIFLNEESYFYLNQSGLVYDNIKKLKDKAQNLANQASNYAEPPWPLSNWM SWVLPILSPLIPIFLLLFFRPCIFHLVSQFIQNHIQAITDHSI (SEQ ID NO: 3) >AJ289711.1 Human endogenous retrovirus H HERV-H/env59- HERV_H_ENV_59-hENVH3: MILAGRAPSNTSTLMKFYSLLLYSLLFSFPFLYHPLPLPSYLHHTINLTHSLPAASNPS LANNCWLCISLSSSAYIAVPTLQTDRATSPVSLHLRTSFNSPHLYPPEELIYFLDRSS KTSPDISHQPAAALLHIYLKNLSPYINSTPPIFGPLTTQTTIPVAAPLCISRQRPTGIPL GNISPSRCSFTLHLQSPTTHVTETIGVFQLHIIDKPSINTDKLKNVSSNYCLGRHLPYI SLHPWLPSPCSSDSPPRPSSCLLTPSPQNNSERLLVDTQRFLIHHENRTSSSMQLA HQSPLQPLTAAALAGSLGVWVQDTPFSTPSHPFSLHLQFCLTQGLFFLCGSSTYMC LPANWTGTCTLVFLTPKIQFANGTKELPVPLMTLTPQKRVIPLIPLMVGLGLSASTIAL STGIAGISTSVTTFRSPSNDFSASITDISQTLSVLQAQVDSLAAVVLQNRRGLGLSILL NEECCFYLNQSGLVYENIKKLKDRAQKLANQASNYAESPWALSNWMSWVLPILSPL IPIFLLLLFGPCIFHLVSQFIQNRIQAITNHSI (SEQ ID NO: 4) >AC074261.3 Homo sapiens chromosome 12 clone RP11-55F19 envK1- ENVK1: MHPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEQMKLPSTKKAEPPTWAQLKK LTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTNWAYVPFPP LIRAVTWMDNPIEVYVNDSVWVHGPIDDRCPAKPEEEGMMINISIGYHYPPICLGRA PGCLMPAVQNWLVEVPTVSPISRFTYNMVSGMSLRPRVNYLQDFSYQRSLKFRPK GKPCPKEIPKESKNTEVLVWEECVANSVVILQNNEFGTIIDWAPRGQFYHNCSGQT QSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPE HPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSLTVPLQSCVKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSI HILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTAMAAVAGVALHSFVQSVNFVNDWQKN STRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQ IYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADG LANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRFTQQLRRDSYHRERAMMTMVVLS KRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 5) >AC072054.10 Homo sapiens BAC clone RP11-33P21-ENVK2: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTYWAYVPFP PLIRAVTWMDNPTEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYHYPPICLGR APGCLMPAVQNWLVEVPTVSPICRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRP KGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHNCSGQ TQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIVSPVSGP EHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTIDLNSSLTVPLQSCVKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPS VHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDWQK NSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITP QIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVAD GLANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRCTQQLRRDSDHRERAMMTMAV LSKRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 6) >Y17833.1 Human endogenous retrovirus K (HERV-K) envK3-ENVK3: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTYWAYVPFP PLIRAVTWMDNPIEVYVNDSVWVPGPTDDHCPAKPEEEGMMINISIGYRYPPICLGR APGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSFKFRP KGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHNCSGQ TQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIISPVSGP EHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSVTVPLQSCIKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWETSPSI HTLTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDWQKN STRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFSITPQ IYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADG LANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRCTQQLRRDSDHRERAMMTMAVLS KRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 7) >AF164615.1 Homo sapiens endogenous retrovirus HERV-K109 envK4- ENVK4: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTNWAYVPFP PLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPICLGRA PGCLMPAVQNWLVEVPIVSPICRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRPK GKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWTPQGQFYHNCSGQT QSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIISPVSGPE HPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSLTLPLQSCVKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPSI HILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDGQKNS TRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQI YNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADG LANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRCTQQLRRDSDHRERAMMTMAVLS KRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 8) >AY037928.1 Human endogenous retrovirus K113 envK5-ENVK5: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTYWAYVPFP PLIRAVTWMDNPIEIYVNDSVWVPGPTDDCCPAKPEEEGMMINISIGYRYPPICLGR APGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRP KGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTLIDWAPRGQFYHNCSGQ TQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTARPKIISPVSGP EHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTIDLNSSLTVPLQSCVKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPS VHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDWQN NSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITP QIYNESEHHWDMVRCHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVAD GLANLNTVTWVKTIGSTTIINLILILVCLFCLLLVYRCTQQLRRDSDHRERAMMTMVVL SKRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 9) >AY037929.1 Human endogenous retrovirus K115 envK6-ENVK6: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAVANYTNWAYVPFP PLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGR APGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRP KGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHNCSGQ TQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKRISTPRPKIVSPVSGP EHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSLTLPLQSCVKPPYMLVV GNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASPS VHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDGQKN STRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQ IYNDSEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADG LANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRCTQQLRRDSDHRERAMMTMAVLS KRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 10) >AC078899.1 Homo sapiens chromosome 19, BAC BC371065 envT-ENVT: MGPEAWVRPLKTAPKPGEAIRLILFIYLSCFFLPVMSSEPSYSFLLTSFTTGRVFANT TWRAGTSKEVSFAVDLCVLFPEPARTHEEQHNLPVIGAGSVDLAAGFGHSGSQTG CGSSKGAEKGLQNVDFYLCPGNHPDASCRDTYQFFCPDWTCVTLATYSGGSTRS STLSISRVPHPKLCTRKNCNPLTITVHDPNAAQWYYGMSWGLRLYIPGFDVGTMFTI QKKILVSWSSPKPIGPLTDLGDPIFQKHPDKVDLTVPLPFLVPRPQLQQQHLQPSLM SILGGVHHLLNLTQPKLAQDCWLCLKAKPPYYVGLGVEATLKRGPLSCHTRPRALTI GDVSGNASCLISTGYNLSASPFQATCNQSLLTSISTSVSYQAPNNTWLACTSGLTR CINGTEPGPLLCVLVHVLPQVYVYSGPEGRQLIAPPELHPRLHQAVPLLVPLLAGLSI AGSAAIGTAALVQGETGLISLSQQVDADFSNLQSAIDILHSQVESLAEVVLQNCRCLD LLFLSQGGLCAALGESCCFYANQSGVIKGTVKKVRENLDRHQQERENNIPWYQSM FNWNPWLTTLITGLAGPLLILLLSLIFGPCILNSFLNFIKQRIASVKLTYLKTQYDTLVN N (SEQ ID NO: 11) >AC000064.1 Human BAC clone RG083M05 from 7q21-7q22 envW (Syncytin-1)- ENVW (Syncytin-1): MALPYHIFLFTVLLPSFTLTAPPPCRCMTSSSPYQEFLWRMQRPGNIDAPSYRSLSK GTPTFTAHTHMPRNCYHSATLCMHANTHYWTGKMINPSCPGGLGVTVCWTYFTQ TGMSDGGGVQDQAREKHVKEVISQLTRVHGTSSPYKGLDLSKLHETLRTHTRLVSL FNTTLTGLHEVSAQNPTNCWICLPLNFRPYVSIPVPEQWNNFSTEINTTSVLVGPLV SNLEITHTSNLTCVKFSNTTYTTNSQCIRWVTPPTQIVCLPSGIFFVCGTSAYRCLNG SSESMCFLSFLVPPMTIYTEQDLYSYVISKPRNKRVPILPFVIGAGVLGALGTGIGGIT TSTQFYYKLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTAERGGTC LFLGEECCYYVNQSGIVTEKVKEIRDRIQRRAEELRNTGPWGLLSQWMPWILPFLG PLAAIILLLLFGPCIFNLLVNFVSSRIEAVKLQMEPKMQSKTKIYRRPLDRPASPRSDV NDIKGTPPEEISAAQPLLRPNSAGSS (SEQ ID NO: 12) >AL136139.6 Human DNA sequence from clone RP4-76112 envFRD-ENVFRD (Syncytin-2): MGLLLLVLILTPSLAAYRHPDFPLLEKAQQLLQSTGSPYSTNCWLCTSSSTETPGTA YPASPREWTSIEAELHISYRWDPNLKGLMRPANSLLSTVKQDFPDIRQKPPIFGPIFT NINLMGIAPICVMAKRKNGTNVGTLPSTVCNVTFTVDSNQQTYQTYTHNQFRHQPR FPKPPNITFPQGTLLDKSSRFCQGRPSSCSTRNFWFRPADYNQCLQISNLSSTAEW VLLDQTRNSLFWENKTKGANQSQTPCVQVLAGMTIATSYLGISAVSEFFGTSLTPLF HFHISTCLKTQGAFYICGQSIHQCLPSNWTGTCTIGYVTPDIFIAPGNLSLPIPIYGNS PLPRVRRAIHFIPLLAGLGILAGTGTGIAGITKASLTYSQLSKEIANNIDTMAKALTTMQ EQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVNQSGKVQDNIRQLLNQA SSLRERATQGWLNWEGTWKWFSWVLPLTGPLVSLLLLLLFGPCLLNLITQFVSSRL QAIKLQTNLSAGRHPRNIQESPF (SEQ ID NO: 13) >AC073210.8 Homo sapiens BAC clone RP11-460N20 envR-ENVR: MLGMNMLLITLFLLLPLSMLKGEPWEGCLHCTHTTWSGNIMTKTLLYHTYYECAGT CLGTCTHNQTTYSVCDPGRGQPYVCYDPKSSPGTWFEIHVGSKEGDLLNQTKVFP SGKDVVSLYFDVCQIVSMGSLFPVIFSSMEYYSSCHKNRYAHPACSTDSPVTTCWD CTTWSTNQQSLGPIMLTKIPLEPDCKTSTCNSVNLTILEPDQPIWTTGLKAPLGARVS GEEIGPGAYVYLYIIKKTRTRSTQQFRVFESFYEHVNQKLPEPPPLASNLFAQLAENI ASSLHVASCYVCGGMNMGDQWPWEARELMPQDNFTLTASSLEPAPSSQSIWFLK TSIIGKFCIARWGKAFTDPVGELTCLGQQYYNETLGKTLWRGKSNNSESPHPSPFS RFPSLNHSWYQLEAPNTWQAPSGLYWICGPQAYRQLPAKWSGACVLGTIRPSFFL MPLKQGEALGYPIYDETKRKSKRGITIGDWKDNEWPPERIIQYYGPATWAEDGMW GYRTPVYMLNRIIRLQAVLEIITNETAGALNLLAQQATKMRNVIYQNRLALDYLLAQE EGVCGKFNLTNCCLELDDEGKVIKEITAKIQKLAHIPVQTWKG (SEQ ID NO: 14) >AC093488.1 Homo sapiens chromosome 3 clone RP11-1008 envR(b)- ENVR(b): MDPLHTIEKVPARRNIHDRGHQGHRMGDGTPGRPKISVQQMTRFSLIIFFLSAPFVV NASTSNVFLQWAHSYADGLQQGDPCWVCGSLPVTNTMELPWWVSPLQGKDWVF FQSFIGDLKQWTGAQMTGVTRKNISEWPINKTLNEPGHDKPFSVNETRDKVIAFAIP LLDTKVFVQTSRPQNTQYRNGFLQIWDGFIWLTATKGHLSQIAPLCWEQRNHSLDN WPNTTRVMGWIPPGQCRHTILLQQRDLFATDWSQQPGLNWYAPNGTQWLCSPNL WPWLPSGWLGCCTLGIPWAQGRWVKTMEVYPYLPHVVNQGTRAIVHRNDHLPTIF MPSVGLGTVIQHIEALANFTQRALNDSLQSISLMNAEVYYMHEDILQNRMALDILTAA EGGTCALIKTECCVYIPNNSRNISLALEDTCRQIQVISSSALSLHDWIASQFSGRPSW WQKILIVLATLWSVGIALCCGLYFCRMFSQHIPQTHSIIFQQELPLSPPSQEHYQSQR DIFHSNAP (SEQ ID NO: 15) >AC016222.4 Homo sapiens clone RP11-26J6 envF(c)2-ENVF(c)2: MNSPCDRLQQFIQVLLEESWSFPSFANTLHWPENLLSYIDELVWQGSLQNFHQHE VRFDKPPLRLPLTGFSSLTENWSSRQAVSSRLVATAASPPAGCQAPIAFLGLKFSSL GPARKNPALCFLYDQSNSKCNTSWVKENVGCPWHWCNIHEALIRTEKGSDPMFYV NTSTGGRDGFNGFNLQISDPWDPRWASGVDGGLYEHKTFMYPVAKIRIARTLKTTV TGLSDLASSIQSAEKELTSQLQPAADQAKSSRFSWLTLISEGAQLLQSTGVQNLSHC FLCAALRRPPLVAVPLPTPFNYTINSSTPIPPVPKGQVPLFSDPIRHKFPFCYSTPNA SWCNQTRMLTSTPAPPRGYFWCNSTLTKVLNSTGNHTLCLPISLIPGLTLYSQDELS HLLAWTEPRPQNKSKWAIFLPLVLGISLASSLVASGLGKGALTHSIQTSQDLSTHLQL AIEASAESLDSLQRQITTVAQVAAQNRQALDLLMAEKGRTCLFLQEECCYYLNESGV VENSLQTLKKKKSSKRS (SEQ ID NO: 16) >AL354685.17 Human DNA sequence from clone RP13-75G22 envF(c)1- ENVF(c)1: MARPSPLCLLLLLTLLTPIVPSNSLLTEPPFRWRFYLHETWTQGNRLSTVTLATVDC QPHGCQAQVTFNFTSFKSVLRGWSNPTICFVYDQTHSNCRDYWVDTNGGCPYAY CRMHVTQLHTAKKLQHTYRLTSDGRTTYFLTIPDPWDSRWVSGVTGRLYRWPTDS YPVGKLRIFLTYIRVIPQVLSNLKDQADNIKHQEEVINTLVQSHPKADMVTYDDKAEA GPFSWITLVRHGARLVNMAGLVNLSHCFLCTALSQPPLVAVPLPQAFNTSGNHTAH PSGVFSEQVPLFRDPLQPQFPFCYTTPNSSWCNQTYSGSLSNLSAPAGGYFWCNF TLTKHLNISSNNTLSRNLCLPISLVPRLTLYSEAELSSLVNPPMRQKRAVFPPLVIGVS LTSSLVASGLGTGAIVHFISSSQDLSIKLQMAIEASAESLASLQRQITSVAKVAMQNR RALDLLTADKGGTCMFLGEECCYYINESGLVETSLLTLDKIRDGLHRPSSTPNYGGG WWQSPLTTWIIPFISPILIICLLLLIAPCVLKFIKNRISEVSRVTVNQMLLHPYSRLPTSE DHYDDALTQQEAAR (SEQ ID NO: 17) HERV-Kcon ENV-hENVKcon: MNPSEMQRKAPPRRRRHRNRAPLTHKMNKMVTSEEQMKLPSTKKAEPPTWAQLK KLTQLATKYLENTKVTQTPESMLLAALMIVSMVVSLPMPAGAAAANYTYWAYVPFP PLIRAVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGR APGCLMPAVQNWLVEVPTVSPISRFTYHMVSGMSLRPRVNYLQDFSYQRSLKFRP KGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHNCSGQ TQSCPSAQVSPAVDSDLTESLDKHKHKKLQSFYPWEWGEKGISTPRPKIVSPVSGP EHPELWRLTVASHHIRIWSGNQTLETRDRKPFYTVDLNSSLTVPLQSCVKPPYMLV VGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP SVHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVALHSSVQSVNFVNDWQ KNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCIT PQIYNESEHHWDMVRRHLQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVA DGLANLNPVTWVKTIGSTTIINLILILVCLFCLLLVCRCTQQLRRDSDHRERAMMTMA VLSKRKGGNVGKSKRDQIVTVSV (SEQ ID NO: 18) HERV-Kcon GAG-hGAGKcon: MGQTKSKIKSKYASYLSFIKILLKRGGVKVSTKNLIKLFQIIEQFCPWFPEQGTLDLKD WKRIGKELKQAGRKGNIIPLTVWNDWAIIKAALEPFQTEEDSVSVSDAPGSCIIDCNE NTRKKSQKETEGLHCEYVAEPVMAQSTQNVDYNQLQEVIYPETLKLEGKGPELVGP SESKPRGTSPLPAGQVPVTLQPQKQVKENKTQPPVAYQYWPPAELQYRPPPESQY GYPGMPPAPQGRAPYPQPPTRRLNPTAPPSRQGSELHEIIDKSRKEGDTEAWQFP VTLEPMPPGEGAQEGEPPTVEARYKSFSIKMLKDMKEGVKQYGPNSPYMRTLLDSI AHGHRLIPYDWEILAKSSLSPSQFLQFKTWWIDGVQEQVRRNRAANPPVNIDADQL LGIGQNWSTISQQALMQNEAIEQVRAICLRAWEKIQDPGSTCPSFNTVRQGSKEPY PDFVARLQDVAQKSIADEKARKVIVELMAYENANPECQSAIKPLKGKVPAGSDVISE YVKACDGIGGAMHKAMLMAQAITGVVLGGQVRTFGGKCYNCGQIGHLKKNCPVLN KQNITIQATTTGREPPDLCPRCKKGKHWASQCRSKFDKNGQPLSGNEQRGQPQAP QQTGAFPIQPFVPQGFQGQQPPLSQVFQGISQLPQYNNCPPPQAAVQQ (SEQ ID NO: 19) Rattus norvegicus & synthetic: APOBEC1-XTEN L8-nspCas9-UGI-SV40 NLS MSSETGPVAVDPTLRRRIEPHEFEVFFDPRELRKETCLLYEINWGGRHSIWRHTSQ NTNKHVEVNFIEKFTTERYFCPNTRCSITWFLSWSPCGECSRAITEFLSRYPHVTLFI YIARLYHHADPRNRQGLRDLISSGVTIQIMTEQESGYCWRNFVNYSPSNEAHWPRY PHLWVRLYVLELYCIILGLPPCLNILRRKQPQLTFFTIALQSCHYQRLPPHILWATGLK SGSETPGTSESATPESDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHS IKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALA HMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLS KSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDL DNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTL LKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVK LNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEK VLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQ LKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTL TLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTIL DFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGIL QTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQI LKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSI DNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGG LSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDF RKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIA KSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFA TVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSP TVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLII KLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDN EQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIH LFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDSG GSTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLL TSDAPEYKPWALVIQDSNGENKIKMLSGGSPKKKRKV (SEQ ID NO: 20) Streptococcus pyogenes: spCas9 Bipartite NLS MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGET AEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHER HPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDL NPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGE KKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADL FLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYK EIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFD NGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAW MTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVY NELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSV EISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKT YAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFM QLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMG RHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNE KLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGK SDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLV ETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINN YHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYF FYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIV KKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEK GKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGR KRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYL DEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKY FDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGSGGGGSGKRTADGS EFEPKKKRKVSSGGDYKDHDGDYKDHDIDYKDDDDK (SEQ ID NO: 21) Staphylococcus aureus: saCas9 MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKR RRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKR RGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRF KTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKE WYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIE NVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENA ELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDE LWHTNDNQIAIFNRLKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKK YGLPNDIIIELAREKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLH DMQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKG NRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFIN RNLVDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYK HHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITP HQIKHIKDFKDYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDND KLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKK DNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKWKLSLKPYRFDVYLDNGVYKFVTV KNLDVIKKENYYEVNSKCYEEAKKLKKISNQAEFIASFYNNDLIKINGELYRVIGVNND LLNRIEVNMIDITYREYLENMNDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHP QIIKKG (SEQ ID NO: 22) Acidaminococcus sp.: asCas12a MTQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYK TYADQCLQLVQLDWENLSAAIDSYRKEKTEETRNALIEEQATYRNAIHDYFIGRTDN LTDAINKRHAEIYKGLFKAELFNGKVLKQLGTVTTTEHENALLRSFDKFTTYFSGFYE NRKNVFSAEDISTAIPHRIVQDNFPKFKENCHIFTRLITAVPSLREHFENVKKAIGIFVS TSIEEVFSFPFYNQLLTQTQIDLYNQLLGGISREAGTEKIKGLNEVLNLAIQKNDETAH IIASLPHRFIPLFKQILSDRNTLSFILEEFKSDEEVIQSFCKYKTLLRNENVLETAEALFN ELNSIDLTHIFISHKKLETISSALCDHWDTLRNALYERRISELTGKITKSAKEKVQRSLK HEDINLQEIISAAGKELSEAFKQKTSEILSHAHAALDQPLPTTLKKQEEKEILKSQLDS LLGLYHLLDWFAVDESNEVDPEFSARLTGIKLEMEPSLSFYNKARNYATKKPYSVEK FKLNFQMPTLASGWDVNKEKNNGAILFVKNGLYYLGIMPKQKGRYKALSFEPTEKT SEGFDKMYYDYFPDAAKMIPKCSTQLKAVTAHFQTHTTPILLSNNFIEPLEITKEIYDL NNPEKEPKKFQTAYAKKTGDQKGYREALCKWIDFTRDFLSKYTKTTSIDLSSLRPSS QYKDLGEYYAELNPLLYHISFQRIAEKEIMDAVETGKLYLFQIYNKDFAKGHHGKPNL HTLYWTGLFSPENLAKTSIKLNGQAELFYRPKSRMKRMAHRLGEKMLNKKLKDQKT PIPDTLYQELYDYVNHRLSHDLSDEARALLPNVITKEVSHEIIKDRRFTSDKFFFHVPI TLNYQAANSPSKFNQRVNAYLKEHPETPIIGIDRGERNLIYITVIDSTGKILEQRSLNTI QQFDYQKKLDNREKERVAARQAWSVVGTIKDLKQGYLSQVIHEIVDLMIHYQAVVV LENLNFGFKSKRTGIAEKAVYQQFEKMLIDKLNCLVLKDYPAEKVGGVLNPYQLTDQ FTSFAKMGTQSGFLFYVPAPYTSKIDPLTGFVDPFVWKTIKNHESRKHFLEGFDFLH YDVKTGDFILHFKMNRNLSFQRGLPGFMPAWDIVFEKNETQFDAKGTPFIAGKRIVP VIENHRFTGRYRDLYPANELIALLEEKGIVFRDGSNILPKLLENDDSHAIDTMVALIRS VLQMRNSNAATGEDYINSPVRDLNGVCFDSRFQNPEWPMDADANGAYHIALKGQL LLNHLKESKDLKLQNGISNQDWLAYIQELRN (SEQ ID NO: 23) Pleckstrin homology domain of Homo sapiens phospholipase C81 (hPLC81) MDSGRDFLTLHGLQDDEDLQALLKGSQLLKVKSSSWRRERFYKLQEDCKTIWQES RKVMRTPESQLFSIEDIQEVRMGHRTEGLEKFARDVPEDRCFSIVFKDQRNTLDLIA PSPADAQHWVLGLHKIIHHSGSMDQRQKLQHWIHSCLRKADKNKDNKMSFKELQN FLKELNIQ (SEQ ID NO: 24) Pleckstrin homology domain of Homo sapiens Akt1 (hAkt) MSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFS VAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQ EEEEMDFRSGSPSDNSGAEEMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVDPPV (SEQ ID NO: 25) Pleckstrin homology domain of Homo sapiens PDPK1 (hPDPK1) KMGPVDKRKGLFARRRQLLLTEGPHLYYVDPVNKVLKGEIPWSQELRPEAKNFKTF FVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSH (SEQ ID NO: 26) Homo sapiens: CD9 Complete Protein MSPVKGGTKCIKYLLFGFNFIFWLAGIAVLAIGLWLRFDSQTKSIFEQETNNNNSSFY TGVYILIGAGALMMLVGFLGCCGAVQESQCMLGLFFGFLLVIFAIEIAAAIWGYSHKD EVIKEVQEFYKDTYNKLKTKDEPQRETLKAIHYALNCCGLAGGVEQFISDICPKKDVL ETFTVKSCPDAIKEVFDNKFHIIGAVGIGIAVVMIFGMIFSMILCCAIRRNREMV (SEQ ID NO: 27) Homo sapiens: CD63 Complete Protein MAVEGGMKCVKFLLYVLLLAFCACAVGLIAVGVGAQLVLSQTIIQGATPGSLLPVVIIA VGVFLFLVAFVGCCGACKENYCLMITFAIFLSLIMLVEVAAAIAGYVFRDKVMSEFNN NFRQQMENYPKNNHTASILDRMQADFKCCGAANYTDWEKIPSMSKNRVPDSCCIN VTVGCGINFNEKAIHKEGCVEKIGGWLRKNVLVVAAAALGIAFVEVLGIVFACCLVKS IRSGYEVM (SEQ ID NO: 28) Homo sapiens: CD81 Complete Protein MGVEGCTKCIKYLLFVFNFVFWLAGGVILGVALWLRHDPQTTNLLYLELGDKPAPNT FYVGIYILIAVGAVMMFVGFLGCYGAIQESQCLLGTFFTCLVILFACEVAAGIWGFVN KDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLK NNLCPSGSNIISNLFKEDCHQKIDDLFSGKLYLIGIAAIVVAVIMIFEMILSMVLCCGIRN SSVY (SEQ ID NO: 29) Homo sapiens: CD47 “Self Hairpin” 10 Amino Acids EVTELTREGE (SEQ ID NO: 30) Homo sapiens: CD47 “Self Hairpin” 21 Amino Acids GNYTCEVTELTREGETIIELK (SEQ ID NO: 31) Homo sapiens: CD47 Complete Protein MWPLVAALLLGSACCGSAQLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYV KWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNY TCEVTELTREGETIIELKYRVVSWFSPNENILIVIFPIFAILLFWGQFGIKTLKYRSGGM DEKTIALLVAGLVITVIVIVGAILFVPGEYSLKNATGLGLIVTSTGILILLHYYVFSTAIGLT SFVIAILVIQVIAYILAVVGLSLCIAACIPMHGPLLISGLSILALAQLLGLVYMKFVE (SEQ ID NO: 32) Synthetic: dDZF1 FKCEHCRILFLDHVMFTIHMGCHGFRDPFKCNMCGEKCDGPVGLFVHMARNAHGE KPFYCEHCEITFRDVVMYSLHKGYHGFRDPFECNICGYHSQDRYEFSSHIVRGEH (SEQ ID NO: 33) Synthetic: dDZF2 HHCQHCDMYFADNILYTIHMGCHSCDDVFKCNMCGEKCDGPVGLFVHMARNAHG EKPTKCVHCGIVFLDEVMYALHMSCHGFRDPFECNICGYHSQDRYEFSSHIVRGEH (SEQ ID NO: 34) Synthetic: DmrA MGRGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLG KQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE (SEQ ID NO: 35) Synthetic: DmrB MASRGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKVDSSRDRNKPFKFML GKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE (SEQ ID NO: 36) Synthetic: DmrC MGSRILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSF NQAYGRDLMEAQEWCRKYMKSGNVKDLLQAWDLYYHVFRRISK (SEQ ID NO: 37) Homo sapiens/Synthetic: FKBP MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQ EVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE (SEQ ID NO: 38) Homo sapiens/Synthetic: FRB QGMLEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAY GRDLMEAQEWCRKYMKSGNVKDLLQAWDLYYHVFRRISK (SEQ ID NO: 39) Synthetic: Anti-GCN4 scFv MGPDIVMTQSPSSLSASVGDRVTITCRSSTGAVTTSNYASWVQEKPGKLFKGLIGG TNNRAPGVPSRFSGSLIGDKATLTISSLQPEDFATYFCALWYSNHWVFGQGTKVEL KRGGGGSGGGGSGGGGSSGGGSEVKLLESGGGLVQPGGSLKLSCAVSGFSLTD YGVNWVRQAPGRGLEWIGVIWGDGITDYNSALKDRFIISKDNGKNTVYLQMSKVRS DDTALYYCVTGLFDYWGQGTLVTVSSYPYDVPDYAGGGGGSGGGGSGGGGSGG GGS (SEQ ID NO: 40) Synthetic: 10x-GCN4 Repeats EELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNY HLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVAR LKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGS GEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKN YHLENEVARLKKGS (SEQ ID NO: 41) Synthetic: 24x-GCN4 Repeats EELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNY HLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVAR LKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGS GEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKN YHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVA RLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGS GEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKN YHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVA RLKKGSGSGEELLSKNYHLENEVARLKKGSGSGEELLSKNYHLENEVARLKKGSGS GEELLSKNYHLENEVARLKKGSGSGEELLSKDYHLENEVARLKKGSGSGEELLSKN YHLENEVARLKKGS (SEQ ID NO: 42) Synthetic: GFP-targeting Nanobody VQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSA GDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYSNVNVGFEYWGQGT QVTVSS (SEQ ID NO: 43) Nostoc punctiforme: Npu DnaE N-terminal Split Intein CLSYETEILTVEYGLLPIGKIVEKRIECTVYSVDNNGNIYTQPVAQWHDRGEQEVFEY CLEDGSLIRATKDHKFMTVDGQMLPIDEIFERELDLMRVDNLPN (SEQ ID NO: 44) Nostoc punctiforme: Npu DnaE C-terminal Split Intein MIKIATRKYLGKQNVYDIGVERDHNFALKNGFIASNCFN (SEQ ID NO: 45) Synthetic: Cfa N-Terminal Split Intein CLSYDTEILTVEYGFLPIGKIVEERIECTVYTVDKNGFVYTQPIAQWHNRGEQEVFEY CLEDGSIIRATKDHKFMTTDGQMLPIDEIFERGLDLKQVDGLP (SEQ ID NO: 46 Synthetic: Cfa C-Terminal Split Intein MVKIISRKSLGTQNVYDIGVEKDHNFLLKNGLVASN (SEQ ID NO: 47) Saccharomyces cerevisiae: Vma N-terminal Split Intein CFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQH RAHKSDSSREVPELLKFTCNATHELWVRTPRSVRRLSRTIKGVEYFEVITFEMGQKK APDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSH VRKATYQTYAPILY (SEQ ID NO: 48) Saccharomyces cerevisiae: Vma C-terminal Split Intein VLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLL ANQVVVHN (SEQ ID NO: 49) Synechocystis sp. PCC 6803: Ssp DnaE N-terminal Split Intein CLSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGEQEVLEY ELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENIKQTEEALDNHRLPFPLL DAGTIK (SEQ ID NO: 50) Synechocystis sp. PCC 6803: Ssp DnaE C-terminal Split Intein MVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAAN (SEQ ID NO: 51) Synthetic: Spy Tag VPTIVMVDAYKRYK (SEQ ID NO: 52) Synthetic: Spy Catcher MVTTLSGLSGEQGPSGDMTTEEDSATHIKFSKRDEDGRELAGATMELRDSSGKTIS TWISDGHVKDFYLYPGKYTFVETAAPDGYEVATAITFTVNEQGQVTVNGEATKGDA HTGSSGS (SEQ ID NO: 53) Bacteriophage MS2: MS2 RNA Binding Protein MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQ NRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLL KDGNPIPSAIAANSGIY (SEQ ID NO: 54) Bacteriophage MS2: MS2 (N55K) RNA Binding Protein MASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQ KRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLL KDGNPIPSAIAANSGIY (SEQ ID NO: 55) Bacteriophage MS2: MS2 (N55K)(V291) RNA Binding Protein MASNFTQFVLVDNGGTGDVTVAPSNFANGIAEWISSNSRSQAYKVTCSVRQSSAQ KRKYTIKVEVPKVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLL KDGNPIPSAIAANSGIY (SEQ ID NO: 56) Bacteriophage PP7: PP7 RNA Binding Protein KTIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKL DQADVVDSGLPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVN LVPLGRS (SEQ ID NO: 57) Bacteriophage Mu: COM RNA Binding Protein MKSIRCKNCNKLLFKADSFDHIEIRCPRCKRHIIMLNACEHPTEKHCGKREKITHSDE TVRY (SEQ ID NO: 58) Synthetic: Zinc Finger ZF6/10 STRPGERPFQCRICMRNFSIPNHLARHTRTHTGEKPFQCRICMRNFSQSAHLKRHL RTHTGEKPFQCRICMRNFSQDVSLVRHLKTHLRQKDGERPFQCRICMRNFSSAQA LARHTRTHTGEKPFQCRICMRNFSQGGNLTRHLRTHTGEKPFQCRICMRNFSQHP NLTRHLKTHLRGS (SEQ ID NO: 59) Synthetic: Zinc Finger ZF8/7 SRPGERPFQCRICMRNFSTMAVLRRHTRTHTGEKPFQCRICMRNFSRREVLENHL RTHTGEKPFQCRICMRNFSQTVNLDRHLKTHLRQKDGERPFQCRICMRNFSKKDH LHRHTRTHTGEKPFQCRICMRNFSQRPHLTNHLRTHTGEKPFQCRICMRNFSVGA SLKRHLKTHLRGS (SEQ ID NO: 60) Synthetic: Zinc Finger ZF9 SRPGERPFQCRICMRNFSDKTKLRVHTRTHTGEKPFQCRICMRNFSVRHNLTRHL RTHTGEKPFQCRICMRNFSQSTSLQRHLKTHLRGF (SEQ ID NO: 61) Synthetic: Zinc Finger MK10 SRPGERPFQCRICMRNFSRRHGLDRHTRTHTGEKPFQCRICMRNFSDHSSLKRHL RTHTGSQKPFQCRICMRNFSVRHNLTRHLRTHTGEKPFQCRICMRNFSDHSNLSR HLKTHTGSQKPFQCRICMRNFSQRSSLVRHLRTHTGEKPFQCRICMRNFSESGHL KRHLRTHLRGS (SEQ ID NO: 62) Synthetic: FokI Zinc Finger Nuclease 17-2 Targeting GFP SRPGERPFQCRICMRNFSTRQNLDTHTRTHTGEKPFQCRICMRNFSRRDTLERHL RTHTGEKPFQCRICMRNFSRPDALPRHLKTHLRGSQLVKSELEEKKSELRHKLKYV PHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDY GVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFL FVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNG EINF (SEQ ID NO: 63) Synthetic: FokI Zinc Finger Nuclease 18-2 Targeting GFP SRPGERPFQCRICMRNFSSPSKLIRHTRTHTGEKPFQCRICMRNFSDGSNLARHLR THTGEKPFQCRICMRNFSRVDNLPRHLKTHLRGSQLVKSELEEKKSELRHKLKYVP HEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYG VIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLF VSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEI NF (SEQ ID NO: 64) Synthetic: FokI Nuclease Domain QLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGK HLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNK HINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIG GEMIKAGTLTLEEVRRKFNNGEINF (SEQ ID NO: 65) Synthetic: AcuI Nuclease Domain VHDHKLELAKLIRNYETNRKECLNSRYNETLLRSDYLDPFFELLGWDIKNKAGKPTN EREVVLEEALKASASEHSKKPDYTFRLFSERKFFLEAKKPSVHIESDNETAKQVRRY GFTAKLKISVLSNFEYLVIYDTSVKVDGDDTFNKARIKKYHYTEYETHFDEICDLLGR ESVYSGNFDKEWLSIENKINHFSVDTL (SEQ ID NO: 66) Synthetic: Truncated AcuI Nuclease Domain YNETLLRSDYLDPFFELLGWDIKNKAGKPTNEREWVLEEALKASASEHSKKPDYTFR LFSERKFFLEAKKPSVHIESDNETAKQVRRYGFTAKLKISVLSNFEYLVIYDTSVKVD GDDT (SEQ ID NO: 67) Ruminococcus flavefaciens: RfxCas13d (CasRx) EASIEKKKSFAKGMGVKSTLVSGSKVYMTTFAEGSDARLEKIVEGDSIRSVNEGEAF SAEMADKNAGYKIGNAKFSHPKGYAWVANNPLYTGPVQQDMLGLKETLEKRYFGE SADGNDNICIQVIHNILDIEKILAEYITNAAYAVNNISGLDKDIIGFGKFSTVYTYDEFKD PEHHRAAFNNNDKLINAIKAQYDEFDNFLDNPRLGYFGQAFFSKEGRNYIINYGNEC YDILALLSGLRHWVVHNNEEESRISRTWLYNLDKNLDNEYISTLNYLYDRITNELTNS FSKNSAANVNYIAETLGINPAEFAEQYFRFSIMKEQKNLGFNITKLREVMLDRKDMS EIRKNHKVFDSIRTKVYTMMDFVIYRYYIEEDAKVAAANKSLPDNEKSLSEKDIFVINL RGSFNDDQKDALYYDEANRIWRKLENIMHNIKEFRGNKTREYKKKDAPRLPRILPAG RDVSAFSKLMYALTMFLDGKEINDLLTTLINKFDNIQSFLKVMPLIGVNAKFVEEYAFF KDSAKIADELRLIKSFARMGEPIADARRAMYIDAIRILGTNLSYDELKALADTFSLDEN GNKLKKGKHGMRNFIINNVISNKRFHYLIRYGDPAHLHEIAKNEAVVKFVLGRIADIQK KQGQNGKNQIDRYYETCIGKDKGKSVSEKVDALTKIITGMNYDQFDKKRSVIEDTGR ENAEREKFKKIISLYLTVIYHILKNIVNINARYVIGFHCVERDAQLYKEKGYDINLKKLE EKGFSSVTKLCAGIDETAPDKRKDVEKEMAERAKESIDSLESANPKLYANYIKYSDE KKAEEFTRQINREKAKTALNAYLRNTKWNVIIREDLLRIDNKTCTLFRNKAVHLEVAR YVHAYINDIAEVNSYFQLYHYIMQRIIMNERYEKSSGKVSEYFDAVNDEKKYNDRLLK LLCVPFGYCIPRFKNLSIEALFDRNEAAKFDKEKKKVSGNSGSG (SEQ ID NO: 68) Ruminococcus flavefaciens & Synthetic: dead RfxCas13d (dCasRx) EASIEKKKSFAKGMGVKSTLVSGSKVYMTTFAEGSDARLEKIVEGDSIRSVNEGEAF SAEMADKNAGYKIGNAKFSHPKGYAWANNPLYTGPVQQDMLGLKETLEKRYFGE SADGNDNICIQVIHNILDIEKILAEYITNAAYAVNNISGLDKDIIGFGKFSTVYTYDEFKD PEHHRAAFNNNDKLINAIKAQYDEFDNFLDNPRLGYFGQAFFSKEGRNYIINYGNEC YDILALLSGLAHWVVANNEEESRISRTWLYNLDKNLDNEYISTLNYLYDRITNELTNS FSKNSAANVNYIAETLGINPAEFAEQYFRFSIMKEQKNLGFNITKLREVMLDRKDMS EIRKNHKVFDSIRTKVYTMMDFVIYRYYIEEDAKVAAANKSLPDNEKSLSEKDIFVINL RGSFNDDQKDALYYDEANRIWRKLENIMHNIKEFRGNKTREYKKKDAPRLPRILPAG RDVSAFSKLMYALTMFLDGKEINDLLTTLINKFDNIQSFLKVMPLIGVNAKFVEEYAFF KDSAKIADELRLIKSFARMGEPIADARRAMYIDAIRILGTNLSYDELKALADTFSLDEN GNKLKKGKHGMRNFIINNVISNKRFHYLIRYGDPAHLHEIAKNEAVVKFVLGRIADIQK KQGQNGKNQIDRYYETCIGKDKGKSVSEKVDALTKIITGMNYDQFDKKRSVIEDTGR ENAEREKFKKIISLYLTVIYHILKNIVNINARYVIGFHCVERDAQLYKEKGYDINLKKLE EKGFSSVTKLCAGIDETAPDKRKDVEKEMAERAKESIDSLESANPKLYANYIKYSDE KKAEEFTRQINREKAKTALNAYLRNTKWNVIIREDLLRIDNKTCTLFANKAVALEVAR YVHAYINDIAEVNSYFQLYHYIMQRIIMNERYEKSSGKVSEYFDAVNDEKKYNDRLLK LLCVPFGYCIPRFKNLSIEALFDRNEAAKFDKEKKKVSGNSGSGPKKKRKVAAAYPY DVPDYA (SEQ ID NO: 69) Synthetic: L17E IWLTALKFLGKHAAKHEAKQQLSKL (SEQ ID NO: 70) Synthetic: L17E-Transmembrane IWLTALKFLGKHAAKHEAKQQLSKLNAVGQDTQEVIVVPHSLPFKVVVISAILALVVLT IISLIILIMLWQKKPR (SEQ ID NO: 71) Synthetic: KALA WEAKLAKALAKALAKHLAKALAKALKACEA (SEQ ID NO: 72) Synthetic: KALA-Transmembrane WEAKLAKALAKALAKHLAKALAKALKACEANAVGQDTQEVIVVPHSLPFKVVVISAIL ALWVLTIISLIILIMLWQKKPR (SEQ ID NO: 73) Synthetic: Vectofusin KKALLHAALAHLLALAHHLLALLKKA (SEQ ID NO: 74) Synthetic: Vectofusin-Transmembrane KKALLHAALAHLLALAHHLLALLKKANAVGQDTQEVIVVPHSLPFKVVVISAILALVVL TIISLIILIMLWQKKPR (SEQ ID NO: 75) Synthetic: Transmembrane Domain NAVGQDTQEVIVPHSLPFKVVVISAILALVVLTIISLIILIMLWQKKPR (SEQ ID NO: 76) Lactococcus lactis: Nisin A ITSISLCTPGCKTGALMGCNMKTATCHCSIHVSK (SEQ ID NO: 77) Lactococcus lactis NIZO 22186: Nisin Z ITSISLCTPGCKTGALMGCNMKTATCNCSIHVSK (SEQ ID NO: 78) Lactococcus lactis subsp. lactis F10: Nisin F ITSISLCTPGCKTGALMGCNMKTATCNCSVHVSK (SEQ ID NO: 79) Lactococcus lactis 61-14: Nisin Q ITSISLCTPGCKTGVLMGCNLKTATCNCSVHVSK (SEQ ID NO: 80) Streptococcus hyointestinalis: Nisin H FTSISMCTPGCKTGALMTCNYKTATCHCSIKVSK (SEQ ID NO: 81) Streptococcus uberis: Nisin U ITSKSLCTPGCKTGILMTCPLKTATCGCHFG (SEQ ID NO: 82) Streptococcus uberis: Nisin U2 VTSKSLCTPGCKTGILMTCPLKTATCGCHFG (SEQ ID NO: 83) Streptococcus galloyticus subsp. pasteurianus: Nisin P VTSKSLCTPGCKTGILMTCAIKTATCGCHFG (SEQ ID NO: 84) L. lactis NZ9800: Nisin A S29A ITSISLCTPGCKTGALMGCNMKTATCHCAIHVSK (SEQ ID NO: 85) L. lactis NZ9800: Nisin A S29D ITSISLCTPGCKTGALMGCNMKTATCHCDIHVSK (SEQ ID NO: 86) L. lactis NZ9800: Nisin A S29E ITSISLCTPGCKTGALMGCNMKTATCHCEIHVSK (SEQ ID NO: 87) L. lactis NZ9800: Nisin A S29G ITSISLCTPGCKTGALMGCNMKTATCHCGIHVSK (SEQ ID NO:8 8) L. lactis NZ9800: Nisin A K22T ITSISLCTPGCKTGALMGCNMTTATCHCSIHVSK (SEQ ID NO: 89) L. lactis NZ9800: Nisin A N20P ITSISLCTPGCKTGALMGCPMKTATCHCSIHVSK (SEQ ID NO: 90) L. lactis NZ9800: Nisin A M21V ITSISLCTPGCKTGALMGCNVKTATCHCSIHVSK (SEQ ID NO: 91) L. lactis NZ9800: Nisin A K22S ITSISLCTPGCKTGALMGCNMSTATCHCSIHVSK (SEQ ID NO: 92) L. lactis NZ9800: Nisin Z N20K ITSISLCTPGCKTGALMGCKMKTATCNCSIHVSK (SEQ ID NO: 93) L. lactis NZ9800: Nisin Z M21K ITSISLCTPGCKTGALMGCNKKTATCNCSIHVSK (SEQ ID NO: 94) AAV2: REP52 MELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAP DYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATT GKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAIL GGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFEL TRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEP KRVRESVAQPSTSDAEASINYADRYQNKCSRHVGMNLMLFPCRQCERMNQNSNIC FTHGQKDCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDD CIFEQ (SEQ ID NO: 95) AAV2: REP78 MPGFYEIVIKVPSDLDEHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAE KLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIR EKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDECYIPNYLLPKTQPELQWAW TNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARY MELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAP DYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATT GKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAIL GGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFEL TRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGGAKKRPAPSDADISEP KRVRESVAQPSTSDAEASINYADRYQNKCSRHVGMNLMLFPCRQCERMNQNSNIC FTHGQKDCLECFPVSESQPVSVVKKAYQKLCYIHHIMGKVPDACTACDLVNVDLDD CIFEQ (SEQ ID NO: 96) AAV2: VP1 MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGP FNGLDKGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSF GGNLGRAVFQAKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQ PARKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGAD GVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYF GYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDG TTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGS QAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQ YLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADN NNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKT NVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVW QDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSA AKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGV YSEPRPIGTRYLTRNL (SEQ ID NO: 97) AAV2: VP2 APGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDADSVPDPQPLGQPP AAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVITTSTR TWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLI NNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGS AHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTF SYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGA SDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGP AMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGS VSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPL MGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKEN SKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL (SEQ ID NO: 98) AAV2: VP3 MATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVITTSTRTWALPTYNNH LYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPK RLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFP ADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFH SSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNW LPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEE KFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNR QAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHP PPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQY TSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL (SEQ ID NO: 99) Relevant RNA Sequences (5'-3') Synthetic: MS2 Stem Loop spCas9 Scaffold RNA for sgRNA with Terminator Example 1 GUUUUAGAGCUAGGCCAACAUGAGGAUCACCCAUGUCUGCAGGGCCUAGCAA GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGGCCAACAUGAGGAUCACCCAU GUCUGCAGGGCCAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 100) Synthetic: MS2 Stem Loop spCas9 Scaffold RNA for sgRNA with Terminator Example 2 GUUUUAGAGCUAGGCCAACAUGAGGAUCACCCAUGUCUGCAGGGCCUAGCAA GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGGCCAACAUGAGGAUCACCCAU GUCUGCAGGGCCAAGUGGCACCGAGUCGGUGCGGGAGCACAUGAGGAUCAC CCAUGUGCGACUCCCACAGUCACUGGGGAGUCUUCCCUUUUUUU (SEQ ID NO: 101) Synthetic: MS2 Stem Loop spCas9 Scaffold RNA for sgRNA with Terminator Example 3 GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCGGGAGCACAUGAGGAUCA CCCAUGUGCGACUCCCACAGUCACUGGGGAGUCUUCCCUUUUUUU (SEQ ID NO: 102) Synthetic: 4xMS2 Stem Loop RNA Scaffold Example UUCUAGAUCAUCGAAACAUGAGGAUCACCCAUAUCUGCAGUCGACAUCGAAA CAUGAGGAUCACCCAUGUCUGCAGUCGACAUCGAAACAUGAGGAUCACCCAU GUCUGCAGUCGACAUCGAAACAUGAGGAUCACCCAUGUCUGCAGUCGACAUC GAAAUCGAUAAGCUUCAGAUCAGAUCCUAG (SEQ ID NO: 103) Synthetic: MS2 Stem Loop Example 1 ACAUGAGGAUCACCCAUGU (SEQ ID NO: 104) Synthetic: MS2 Stem Loop Example 2 ACAUGAGGAUCACCCAUAU (SEQ ID NO: 105) Synthetic: MS2 Stem Loop Example 3 CCACAGUCACUGGG (SEQ ID NO: 106) Synthetic: 2xMS2 Stem Loop Example ACAUGAGGAUCACCCAUGUCUGCAGGGCCUAGCAAGUUAAAAUAAGGCUAGU CCGUUAUCAACUUGGCCAACAUGAGGAUCACCCAUGU (SEQ ID NO: 107) Synthetic: 2xPP7 Stem Loop spCas9 Scaffold RNA for sgRNA with Terminator Example GUUUUAGAGCUAGGCCGGAGCAGACGAUAUGGCGUCGCUCCGGCCUAGCAA GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGGCCGGAGCAGACGAUAUGGCG UCGCUCCGGCCAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 108) Synthetic: PP7 Stem Loop Example GCCGGAGCAGACGAUAUGGCGUCGCUCCGGCC (SEQ ID NO: 109) Synthetic: COM Stem Loop spCas9 Scaffold RNA for sgRNA with Terminator Example GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCCUGAAUGCCUGCGAGCAU CUUUUUUU (SEQ ID NO: 110) Synthetic: COM Stem Loop Example CUGAAUGCCUGCGAGCAUC (SEQ ID NO: 111) Relevant DNA Sequences (5′-3′) Synthetic: Zinc Finger ZF6/10 Binding Site GAAGAAGCTGCAGGAGGT (SEQ ID NO: 112) Synthetic: Zinc Finger ZF8/7 Binding Site GCTGGAGGGGAAGTGGTC (SEQ ID NO: 113) Synthetic: Zinc Finger ZF6/10 & ZF8/7 Binding Site GAAGAAGCTGCAGGAGGTGCTGGAGGGGAAGTGGTC (SEQ ID NO: 114) Synthetic: Zinc Finger ZF6/10 & ZF8/7 Binding Site 8x Repeat Example TGAAGAAGCTGCAGGAGGTGCTGGAGGGGAAGTGGTCCGGATCTTGAAGAAG CTGCAGGAGGTGCTGGAGGGGAAGTGGTCCGGATCTTGAAGAAGCTGCAGGA GGTGCTGGAGGGGAAGTGGTCCGGATCTTGAAGAAGCTGCAGGAGGTGCTGG AGGGGAAGTGGTCCGGATCTTGAAGAAGCTGCAGGAGGTGCTGGAGGGGAAG TGGTCCGGATCTTGAAGAAGCTGCAGGAGGTGCTGGAGGGGAAGTGGTCCGG ATCTTGAAGAAGCTGCAGGAGGTGCTGGAGGGGAAGTGGTCCGGATCTTGAAG AAGCTGCAGGAGGTGCTGGAGGGGAAGTGGTCC (SEQ ID NO: 115) Synthetic: Zinc Finger ZF9 Binding Site GTAGATGGA (SEQ ID NO: 116) Synthetic: Zinc Finger MK10 Binding Site CGGCGTAGCCGATGTCGCGC (SEQ ID NO: 117) Synthetic: Zinc Finger 268 Binding Site AAGGGTTCA (SEQ ID NO: 118) Synthetic: Zinc Finger NRE Binding Site GCGTGGGCG (SEQ ID NO: 119) Synthetic: Zinc Finger 268/NRE or 268//NRE Binding Site Example 1 AAGGGTTCAGCGTGGGCG (SEQ ID NO: 120) Synthetic: Zinc Finger 268/NRE or 268//NRE Binding Site Example 2 AAGGGTTCAGGCGTGGGCG (SEQ ID NO: 121) Synthetic: Zinc Finger 268/NRE or 268//NRE Binding Site Example 3 AAGGGTTCAGTGCGTGGGCG (SEQ ID NO: 122) Synthetic: Fokl Zinc Finger Nuclease 17-2 & 18-2 Binding Site in GFP GATCCGCCACAACATCGAGGACGGCA (SEQ ID NO: 123)

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Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

What is claimed is:
 1. A method of engineering a target cell, the method comprising contacting a particle to the target cell, wherein the particle comprises: (a) a phospholipid bilayer membrane; (b) a gag protein from a human endogenous retrovirus (HERV) or encoded by a HERV GAG consensus sequence, wherein the gag protein is encapsulated within the phospholipid bilayer membrane; and (c) a therapeutic cargo encapsulated within the phospholipid bilayer membrane, wherein the therapeutic cargo is fused with a gag protein or a plasma membrane recruitment domain.
 2. The method of claim 1, wherein the particle does not comprise a non-human gag protein.
 3. The method of claim 1, wherein the particle does not comprise a non-human pol protein.
 4. The method of claim 1, wherein the therapeutic cargo comprises a protein, a RNA, a DNA, or a combination thereof.
 5. The method of claim 1, wherein the therapeutic cargo comprises a gene editing reagent or a polynucleotide that encodes the gene editing agent.
 6. The method of claim 5, wherein the gene editing reagent comprises a zinc finger (ZF), transcription activator-like effector (TALE), a CRISPR-based genome editing or modulating protein; or a ribonucleoprotein complex (RNP) comprising the CRISPR-based genome editing or modulating protein.
 7. The method of claim 5, wherein the gene editing reagent comprises an RNA guided protein.
 8. The method of claim 5, wherein the gene editing reagent comprises a guide RNA.
 9. The method of claim 1, wherein the phospholipid bilayer membrane is attached with a HERV-derived glycoprotein.
 10. The method of claim 9, wherein the HERV-derived glycoprotein is fused to a targeting polypeptide.
 11. The method of claim 10, wherein the targeting polypeptide comprises a single-chain variable fragment (ScFv).
 12. The method of claim 1, wherein the therapeutic cargo is fused with the gag protein.
 13. The method of claim 12, wherein the gag protein is a human endogenous gag protein.
 14. The method of claim 1, wherein the therapeutic cargo is fused with the plasma membrane recruitment domain.
 15. The method of claim 14, wherein the plasma membrane recruitment domain is a human plasma membrane recruitment domain.
 16. The method of claim 14, wherein the plasma membrane recruitment domain comprises a pleckstrin homology (PH) domain.
 17. The method of claim 16, wherein the PH domain is selected from the group consisting of a Pleckstrin homology domain of phospholipase CM (PLCM), Pleckstrin homology domain of Akt1 (Akt1) or a mutant thereof, and Pleckstrin homology domain of PDPK1 (PDPKI).
 18. The method of claim 16, wherein the PH domain is a mutant pleckstrin homology domain of AKT that comprises an amino acid substitution relative to a corresponding wild type Pleckstrin homology domain of Akt1.
 19. The method of claim 18, wherein the amino acid substitution comprises an amino acid substitution of amino acid residue E17 relative to the corresponding wild type pleckstrin homology domain of Akt1
 20. The method of claim 18, wherein the amino acid substitution is E17K.
 21. The method of claim 14, wherein the plasma membrane recruitment domain comprises an amino acid sequence of CD9, CD47, CD63, or CD81.
 22. The method of claim 14, wherein the plasma membrane recruitment domain comprises the amino acid sequence set forth in any one of SEQ ID NO: 19 or 24-32.
 23. The method of claim 1, wherein the particle comprises the gag protein from a HERV.
 24. The method of claim 23, wherein the gag protein is encoded comprises GAG sequence of HERV-K113, HERV-K101, HERV-K102, HERV-K104, HERV-K107, HERV-K108, HERV-K109, HERV-K115, HERV-K11p22, or HERV-K12q13 protein.
 25. The method of claim 1, wherein the particle comprises the gag protein encoded by HERV GAG consensus sequence.
 26. The method of claim 25, wherein the gag protein is encoded by the sequence of SEQ ID NO:
 19. 27. The method of claim 1, wherein the target cell is in vitro.
 28. The method of claim 1, wherein the target cell is in vivo. 